Polypeptides having cellulolytic enhancing activity and uses thereof

ABSTRACT

The invention relates to a polypeptide having cellulolytic enhancing activity, wherein the polypeptide is selected from the group consisting of: (a) a polypeptide comprising an amino acid sequence having at least 60% sequence identity with the amino acid sequence of SEQ ID NO: 2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44 and/or 47; (b) a polypeptide encoded by a polynucleotide comprising a nucleotide sequence having at least 60% sequence identity to the nucleotide sequence of SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45 and/or 48; (c) a polypeptide encoded by a polynucleotide comprising a nucleotide sequence which hybridises under at least high stringency conditions with the complementary strand of SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45 and/or 48; and (d) a fragment of the polypeptide of (a), (b), or (c), that has cellulolytic enhancing activity.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Continuation of U.S. application Ser. No.16/318,776, filed 18 Jan. 2019, which is a National Stage entry ofInternational Application No. PCT/EP2017/069049, filed 27 Jul. 2017,which claims priority to European Patent Application Nos. 16181977.6,16181978.4, 16181980.0, 16181985.9, 16181982.6, 16181984.2, 16181987.5,16181991.7, 16181919.8, 16181920.6, 16181921.4, 16181922.2, 16181927.1,16181929.7, 16181930.5, and 16181931.3, all filed 29 Jul. 2016.

REFERENCE TO SEQUENCE LISTING SUBMITTED AS A COMPLIANT ASCII TEXT FILE(.txt)

Pursuant to the EFS-Web legal framework and 37 CFR §§ 1.821-825 (seeMPEP § 2442.03(a)), a Sequence Listing in the form of an ASCII-complianttext file (entitled “Sequence_Listing_2919208-495001_ST25.txt” createdon 28 Dec. 2020, and 91,426 bytes in size) is submitted with the instantapplication, and the entire contents of the Sequence Listing areincorporated herein by reference.

BACKGROUND Field of the Invention

The invention relates to a polypeptide having cellulolytic enhancingactivity and to variants and fragments thereof. Moreover, the inventionrelates to polynucleotides encoding the polypeptide and to variants andfragments thereof. Also included in the invention are nucleic acidconstructs and cells comprising such a polynucleotide as well as methodsfor producing and using the polypeptides, variants and fragmentsthereof. The invention further concerns compositions comprising thepolypeptides, variants and fragments thereof and to processes in whichthey are used.

Description of Related Art

Carbohydrates constitute the most abundant organic compounds on earth.However, much of this carbohydrate is sequestered in complex polymersincluding starch and a collection of carbohydrates and lignin known aslignocellulose. The main carbohydrate components of lignocellulose arecellulose, hemicellulose and pectins. These complex polymers are oftenreferred to collectively as lignocellulose.

Bioconversion of lignocellulosic biomass to a sugar that is subsequentlyfermented to produce alcohol as an alternative to liquid fuels hasattracted an intensive attention of researchers since 1970s, when theoil crisis broke out because of decreasing the output of petroleum byOPEC.

Ethanol has been widely used as a 10% blend to gasoline in the USA or asa neat fuel for vehicles in Brazil in the last two decades. Morerecently, the use of E85, an 85% ethanol blend has been implementedespecially for clean city applications. The importance of biofuel willincrease in parallel with increases in prices for oil and the gradualdepletion of its sources.

Additionally, fermentable sugars are being used to produce plastics,polymers and other bio-based products and this industry is expected togrow substantially, therefore increasing the demand for abundant lowcost fermentable sugars which can be used as a feedstock in lieu ofpetroleum-based feedstocks.

The sequestration of large amounts of carbohydrates in plant biomassprovides a plentiful source of potential energy in the form of sugars,both five carbon and six carbon sugars, that could be utilized fornumerous industrial processes. However, the enormous energy potential ofthese carbohydrates is currently under-utilized, because the sugars arelocked in complex polymers and hence are not readily accessible forfermentation.

Regardless of the type of cellulosic feedstock, the cost and hydrolyticefficiency of enzymes are major factors that restrict thecommercialization of the biomass bioconversion processes. The productioncosts of microbially produced enzymes are tightly connected withproductivity of the enzyme-producing strain, the specific activity ofthe enzymes, the mode of action of the enzyme and the final activityyield in the fermentation broth.

In spite of the continued research of the last few decades to understandenzymatic lignocellulosic biomass degradation and enzyme production, itremains desirable to discover or to engineer new highly active enzymesand enzyme compositions that can be used to degrade (ligno)cellulosicmaterial. The present invention provides such enzymes.

SUMMARY OF THE INVENTION

The present invention provides a polypeptide which has the ability tomodify a cellulosic material. The present invention providespolypeptides having cellulolytic enhancing activity and polynucleotidesencoding the polypeptides of the invention. The polypeptides of theinvention may have lytic polysaccharide monooxygenase (LPMO) activity.

The polypeptides of the present invention may be used in industrialprocesses such as the degradation of cellulosic material. They may alsobe used in the production of sugar from cellulosic material.

Sugars produced in this way may be used in fermentation processes.Accordingly, the invention also provides a process for producing afermentation product, such as ethanol.

The polypeptides of the current invention may also be used, for example,in the preparation of a food product, in the preparation of a detergent,in the preparation of an animal feed product, in the treatment of pulp,in the manufacture of paper or in the preparation of a fabric or textileor in the cleaning thereof.

According to the invention, there is thus provided a polypeptide havingcellulolytic enhancing activity, wherein the polypeptide is selectedfrom the group consisting of:

-   -   (a) a polypeptide comprising an amino acid sequence having at        least 60% sequence identity with the amino acid sequence of SEQ        ID NO: 2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44        and/or 47;    -   (b) a polypeptide encoded by a polynucleotide comprising a        nucleotide sequence having at least 60% sequence identity to the        nucleotide sequence of SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24,        27, 30, 33, 36, 39, 42, 45 and/or 48,    -   (c) a polypeptide encoded by a polynucleotide comprising a        nucleotide sequence which hybridises under at least high        stringency conditions with the complementary strand of SEQ ID        NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45        and/or 48, and    -   (d) a fragment of the polypeptide of (a), (b), or (c), that has        cellulolytic enhancing activity.

The invention further provides:

a polynucleotide, wherein the polynucleotide comprises a nucleotidesequence that is selected from the group consisting of:

-   -   (a) a nucleotide sequence having at least 60% sequence identity        with the nucleotide sequence of SEQ ID NO: 3, 6, 9, 12, 15, 18,        21, 24, 27, 30, 33, 36, 39, 42, 45 and/or 48,    -   (b) a nucleotide sequence which hybridises under at least high        stringency conditions with the complementary strand of SEQ ID        NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45        and/or 48,    -   (c) a fragment which is at least 100 nucleotides in length of a        nucleotide sequence as defined in (a) or (b),    -   (d) a nucleotide sequence which is degenerate as a result of the        genetic code to a nucleotide sequence as defined in any one of        (a), (b), or (c), and    -   (e) a nucleotide sequence which is the complement of a        nucleotide sequence as defined in (a), (b), (c), or (d);

a nucleic acid construct comprising a polynucleotide of the invention;

a host cell comprising a polypeptide, a polynucleotide or a nucleic acidconstruct according to the invention;

a process for producing a polypeptide of the invention, which processcomprises the steps of:

-   -   (a) cultivating a host cell according to the invention under        conditions conducive to the production of the polypeptide, and    -   (b) optionally, recovering the polypeptide;        -   a composition comprising:    -   (a) a polypeptide of the invention, and    -   (b) a cellulase and/or a hemicellulase and/or a pectinase;        -   a process for degrading cellulosic material, the process            comprising the step of contacting the cellulosic material            with a polypeptide or a composition of the invention; and        -   a process for producing a fermentation product, the process            comprising the steps of:    -   (a) enzymatically hydrolysing a cellulosic material with a        polypeptide or a composition of the invention,    -   (b) fermenting the enzymatically hydrolysed cellulosic material        to produce a fermentation product, and    -   (c) optionally, recovering of the fermentation product.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 sets out a schematic representation of the Aspergillus expressionvector pGBFIN-50.

FIG. 2 sets out a schematic representation of the RasamsoniaCre-recombinase expression vector pEBA521.

BRIEF DESCRIPTION OF THE SEQUENCES

SEQ ID NOs: 1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46set out full-length amino acid sequences (including signal peptide) ofthe polypeptides of the invention.

SEQ ID NOs: 2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44, 47set out mature amino acid sequences of the polypeptides of theinvention.

SEQ ID NOs: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48set out nucleotide sequences (including stop codon) encoding thefull-length polypeptides of the invention (SEQ ID NO: 1).

DETAILED DESCRIPTION OF A PREFERRED EMBODIMENT

Throughout the present specification and the accompanying claims, thewords “comprise” and “include” and variations such as “comprises”,“comprising”, “includes” and “including” are to be interpretedinclusively. That is, these words are intended to convey the possibleinclusion of other elements or integers not specifically recited, wherethe context allows.

The articles “a” and “an” are used herein to refer to one or to morethan one (i.e. to one or at least one) of the grammatical object of thearticle. By way of example, “an element” may mean one element or morethan one element.

The term “derived from” also includes the terms “originated from”,“obtained from”, “obtainable from”, “isolated from”, and “created from”,and generally indicates that one specified material find its origin inanother specified material or has features that can be described withreference to the other specified material. As used herein, a substance(e.g. a nucleic acid molecule or polypeptide) “derived from” amicroorganism preferably means that the substance is native to thatmicroorganism.

Polypeptide

The present invention provides a polypeptide which has the ability tomodify a cellulosic material. The present invention provides apolypeptide which has the ability to degrade cellulosic material. In anembodiment, the polypeptide of the present invention has cellulolyticenhancing activity. In an embodiment the polypeptide of the presentinvention has LPMO activity. In an embodiment the polypeptide of thepresent invention is an isolated polypeptide.

Endo-1,4-β-glucanases (EG) and exo-cellobiohydrolases (CBH) catalyze thehydrolysis of insoluble cellulose to cellooligosaccharides (cellobioseas a main product), while β-glucosidases (BGL) convert theoligosaccharides, mainly cellobiose and cellotriose, to glucose.

Xylanases together with other accessory enzymes, for exampleα-L-arabinofuranosidases, feruloyl and acetyl-xylan esterases,glucuronidases, and β-xylosidases catalyze the hydrolysis of part of thehemicelluloses.

Pectic substances include pectins, arabinans, galactans andarabinogalactans. Pectins are the most complex polysaccharides in theplant cell wall. They are built up around a core chain of α(1,4)-linkedD-galacturonic acid units interspersed to some degree with L-rhamnose.In any one cell wall there are a number of structural units that fitthis description and it has generally been considered that in a singlepectic molecule the core chains of different structural units arecontinuous with one another.

Pectinases include, for example an endo-polygalacturonase, a pectinmethyl esterase, an endo-galactanase, a β-galactosidase, a pectin acetylesterase, an endo-pectin lyase, pectate lyase, α-rhamnosidase, anexo-galacturonase, an exo-polygalacturonate lyase, a rhamnogalacturonanhydrolase, a rhamnogalacturonan lyase, a rhamnogalacturonan acetylesterase, a rhamnogalacturonan galacturonohydrolase, axylogalacturonase, an α-arabinofuranosidase.

Lytic polysaccharide monooxygenases (LPMO) are recently classified byCAZy in family AA9 (Auxiliary Activity Family 9), family AA10 (AuxiliaryActivity Family 10), family AA11 (Auxiliary Activity Family 11) orfamily AA13 (Auxiliary Activity Family 13). Lytic polysaccharidemonooxygenases are able to open a crystalline glucan structure. Lyticpolysaccharide monooxygenases may also affect cello-oligosaccharides.PMO and LPMO are used herein interchangeably. Often in literature theseproteins are mentioned to enhance the action of cellulases on cellulosicmaterial, i.e. have cellulolytic enhancing activity. Thus, a polypeptideof the invention may be one which enhances the hydrolysis of acellulosic material by proteins having cellulolytic activity.

As set out above, a polypeptide of the invention will typically havecellulolytic enhancing activity. In an embodiment they will have LPMOactivity. In an embodiment they display catalytic activity via anoxidative cleavage reaction on cellulosic material.

The polypeptides of the invention may however also have one or morealternative and/or additional activities as mentioned above. Also, acomposition of the invention as described herein may comprise one ormore of the activities mentioned above in addition to the activityprovided by the polypeptide of the invention.

In an embodiment the polypeptide of the present invention hascellulolytic enhancing activity, wherein the polypeptide is selectedfrom the group consisting of (a) a polypeptide comprising an amino acidsequence having at least 60% sequence identity with the amino acidsequence of SEQ ID NO: 2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38,41, 44 and/or 47, (b) a polypeptide encoded by a polynucleotidecomprising a nucleotide sequence having at least 60% sequence identityto the nucleotide sequence of SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24,27, 30, 33, 36, 39, 42, 45 and/or 48, (c) a polypeptide encoded by apolynucleotide comprising a nucleotide sequence which hybridises underat least high stringency conditions with the complementary strand of SEQID NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45 and/or48, and (d) a fragment of the polypeptide of (a), (b), or (c), that hascellulolytic enhancing activity.

Advantageously, the polypeptide of the invention has cellulolyticenhancing activity. The polypeptide of the invention may enhance thehydrolysis of a cellulosic material catalyzed by one or morepolypeptides having cellulolytic activity by reducing the amount ofcellulolytic enzyme required to reach the same degree of hydrolysis,preferably at least 1.01-fold, e.g., at least 1.05-fold, at least1.10-fold, at least 1.25-fold, at least 1.5-fold, at least 2-fold, atleast 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, or atleast 20-fold.

The cellulolytic enhancing activity can be determined by measuring theincrease in sugar release (e.g. glucose release) during hydrolysis of acellulosic material by a cellulolytic enzyme composition (e.g. theRasamsonia enzyme compositions as used in the Examples or commercialenzyme compositions such as Celluclast® combined with Novozyme 188(obtainable from Novozymes, Denmark or Sigma-Aldrich®, USA),Accellerase® 1000 (obtainable from Genencor, USA or Sigma-Aldrich®,USA), and Methaplus® (obtainable from DSM, The Netherlands)) in thepresence or absence of a polypeptide of the present invention.

In an embodiment a polypeptide of the invention may be added on top ofthe enzyme composition. Alternatively, a polypeptide of the inventionmay be replacing part of the enzyme composition by an equal amount(based on protein). Typical conditions include using 0.9 mg/g dry matterof acid-pretreated corn stover of the polypeptide of the invention ontop of 1.6 mg/g dry matter of acid-pretreated corn stover of acellulolytic enzyme composition (comprising 0.225 mg/g dry matter ofacid-pretreated corn stover of beta-glucosidase (SEQ ID NO:2 from WO2012/000890), 0.75 mg/g dry matter of acid-pretreated corn stover ofcellobiohydrolase I (SEQ ID NO: 2 from WO 2010/122141), 0.625 mg/g drymatter of acid-pretreated corn stover of cellobiohydrolase II (SEQ IDNO: 2 from WO 2011/098580)) in a hydrolysis for 72 hours at pH 4.5 and atemperature of 62° C.

Dilute-acid pre-treated corn stover may be obtained as described inSchell, D. J., Applied Biochemistry and Biotechnology (2003), vol.105-108, pp 69-85. A pilot scale pretreatment reactor can be usedoperating at steady state conditions of 190° C., 1 min residence timeand an effective H₂SO₄ acid concentration of 1.45% (w/w) in the liquidphase. For the preparation of low acid pretreated corn stover, alsoreferred to as mildly pretreated corn stover, a pilot scale pretreatmentreactor may be used operating at steady state conditions of 182° C., 4.7min residence time and an effective H₂SO₄ acid concentration of 0.35%(w/w) in the liquid aiming at a pH of 2.5.

According to a preferred embodiment the polypeptide of the invention isa “thermostable” enzyme. In another preferred embodiment, thepolynucleotide according to the invention encodes a “thermostable”enzyme. Herein, “thermostable” enzyme means that the enzyme has atemperature optimum of 60° C. or higher. In an embodiment the enzyme hasa temperature optimum of 65° C. or higher, 70° C. or higher, 75° C. orhigher, 80° C. or higher, or 85° C. or higher. In general, thetemperature optimum will be lower than 95° C. The temperature optimumcan be measured when using the enzyme in a hydrolysis for 72 hours atoptimum pH conditions.

According to a preferred embodiment the polypeptide of the invention hasa pH optimum in between pH 2 and pH 8. Preferably, the enzyme has a pHoptimum of 6 or lower, 5.5 or lower, 5.0 or lower, 4.5 or lower, 4.0 orlower, or 3.5 or lower. Preferably, the enzyme has a pH optimum of 2.0or higher, preferably 2.5 or higher. The pH optimum can be measured whenusing the enzyme in a hydrolysis for 72 hours at optimum temperatureconditions.

In an embodiment the polypeptide of the invention comprises an aminoacid sequence having at least 60% sequence identity with the amino acidsequence of SEQ ID NO: 1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37,40, 43 and/or 46 or SEQ ID NO: 2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32,35, 38, 41, 44 and/or 47. In an embodiment the polypeptide of theinvention comprises an amino acid sequence having at least 65% sequenceidentity, at least 70% sequence identity, at least 75% sequenceidentity, at least 76% sequence identity, at least 77% sequenceidentity, at least 78% sequence identity, at least 79% sequenceidentity, at least 80% sequence identity, at least 81% sequenceidentity, at least 82% sequence identity, at least 83% sequenceidentity, at least 84% sequence identity, at least 85% sequenceidentity, at least 86% sequence identity, at least 87% sequenceidentity, at least 88% sequence identity, at least 89% sequenceidentity, at least 90% sequence identity, at least 91% sequenceidentity, at least 92% sequence identity, at least 93% sequenceidentity, at least 94% sequence identity, at least 95% sequenceidentity, at least 96% sequence identity, at least 97% sequenceidentity, at least 98% sequence identity, at least 99% sequenceidentity, with the amino acid sequence of SEQ ID NO: 1, 4, 7, 10, 13,16, 19, 22, 25, 28, 31, 34, 37, 40, 43 and/or 46 or SEQ ID NO: 2, 5, 8,11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44 and/or 47. In anembodiment the polypeptide of the invention comprises or consists of theamino acid sequence of SEQ ID NO: 1, 4, 7, 10, 13, 16, 19, 22, 25, 28,31, 34, 37, 40, 43 or 46 or SEQ ID NO: 2, 5, 8, 11, 14, 17, 20, 23, 26,29, 32, 35, 38, 41, 44 or 47. SEQ ID NO: 2, 5, 8, 11, 14, 17, 20, 23,26, 29, 32, 35, 38, 41, 44 and 47 are the mature forms of thepolypeptides set out by amino acid sequences SEQ ID NO: 1, 4, 7, 10, 13,16, 19, 22, 25, 28, 31, 34, 37, 40, 43 and 46, respectively.

The invention also features biologically active fragments of thepolypeptides according to the invention. Biologically active fragmentsof a polypeptide of the invention include polypeptides comprising aminoacid sequences sufficiently identical to or derived from the amino acidsequence of SEQ ID NO: 1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37,40, 43 and/or 46 or SEQ ID NO: 2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32,35, 38, 41, 44 and/or 47, which include fewer amino acids than thefull-length polypeptides as given in SEQ ID NO: 1, 4, 7, 10, 13, 16, 19,22, 25, 28, 31, 34, 37, 40, 43 and/or 46 or SEQ ID NO: 2, 5, 8, 11, 14,17, 20, 23, 26, 29, 32, 35, 38, 41, 44 and/or 47, but which exhibit atleast one biological activity of the corresponding full-lengthpolypeptide. Typically, biologically active fragments comprise a domainor motif with at least one activity of the polypeptide of the invention.A biologically active fragment of a polypeptide of the invention can bea polypeptide which is, for example, about 10, about 25, about 50, about100 or more amino acids in length or at least about 100 amino acids, atleast 150, 200, 250, 300, 350, 400 amino acids in length, or of a lengthup to the total number of amino acids of the polypeptide of theinvention. Moreover, other biologically active portions, in which otherregions of the polypeptide are deleted, can be prepared by recombinanttechniques and evaluated for one or more of the biological activities ofthe native form of a polypeptide of the invention. The invention alsofeatures nucleic acid fragments which encode the above biologicallyactive fragments of the polypeptide of the invention.

In an embodiment the polypeptide of the invention is improved. Improvedpolypeptides are polypeptides, wherein at least one biological activityis improved compared to the polypeptides known in the art, such as awild type polypeptide.

The cellulolytic enhancing activity of the polypeptide of the inventionmay be analysed according to the assays as described in the Examples.

A polypeptide of the invention may have one or more improved properties,such as enhanced thermostability, enhanced activity in presence ofdissolved glucose, enhanced activity in presence of dissolved gluconicacid, enhanced activity in presence of dissolved ammonium sulphate,enhanced activity in presence of dissolved sodium chloride, enhancedactivity in presence of ethanol, enhanced activity in presence ofdimethyl sulfoxide (DMSO) or the ability to be produced at higher titersin the heterologous expression organisms Aspergillus niger orTalaromyces emersonii.

The properties of a polypeptide of the invention may be determined usingthe assay described above.

As used herein, the term “polypeptide” refers to a molecule comprisingamino acid residues linked by peptide bonds and containing more thanfive amino acid residues. The amino acids are identified by either thesingle letter or three letter designations. The term “protein” as usedherein is synonymous with the term “polypeptide” and may also refer totwo or more polypeptides. Thus, the terms “protein”, “peptide” and“polypeptide” can be used interchangeably. Polypeptides may optionallybe modified (e.g., glycosylated, phosphorylated, acylated, farnesylated,prenylated, sulfonated, and the like) to add functionality. Polypeptidesexhibiting activity may be referred to as enzymes. It will be understoodthat, as a result of the degeneracy of the genetic code, a multitude ofnucleotide sequences encoding a given polypeptide may be produced.

The term “mature polypeptide” or “mature form of a polypeptide” isdefined herein as a polypeptide in its final form and is obtained aftertranslation of mRNA into polypeptide and post-translationalmodifications of the polypeptide. Post-translational modificationsinclude N-terminal processing, C-terminal truncation, glycosylation,phosphorylation and removal of leader sequences such as signal peptides,pro-peptides and/or prepro-peptides by cleavage.

The term “a fragment of the polypeptide” is defined herein as apolypeptide having one or more amino acids deleted from the amino and/orcarboxyl terminus of the parent polypeptide or a homologous sequencethereof. The term refers to biologically active fragments. The fragmenthas cellulolytic enhancing activity. As indicated herein the fragmentmay be for example, about 10, about 25, about 50, about 100 or moreamino acids in length or at least about 100 amino acids, at least 150,200, 250, 300, 350, 400 amino acids in length, or may be of a length upto the total number of amino acids of the polypeptide of the invention.

The term “prepro-peptide” is defined herein as a signal peptide andpro-peptide present at the amino terminus of a polypeptide, where thepro-peptide is linked (or fused) in frame to the amino terminus of apolypeptide and the signal peptide is linked in frame (or fused) to theamino terminus of the pro-peptide region. The term “signal peptide” isdefined herein as a peptide linked (fused) in frame to the aminoterminus of a polypeptide and directs the polypeptide into the cellsecretory pathway. A pro-peptide may be present between the signalpeptide and the amino terminus of the polypeptide. The term“pro-peptide” is an amino acid sequence linked (fused) in frame to theamino terminus of a polypeptide having biological activity, wherein theresultant polypeptide is known as a proenzyme or pro-polypeptide (or azymogen in some cases), A pro-polypeptide is generally biologicallyinactive and can be converted to a mature active polypeptide bycatalytic or autocatalytic cleavage of the pro-peptide from thepro-polypeptide.

A peptide or polypeptide that is a variant of the polypeptide of thepresent invention, such as a functional equivalent, is also comprisedwithin the present invention. The above polypeptides are collectivelycomprised in the term “polypeptides according to the invention”.

As used herein, the terms “variant, “derivative”, “mutant” or“homologue” can be used interchangeably. They can refer to eitherpolypeptides or polynucleotides. Variants include substitutions,insertions, deletions, truncations, transversions, and/or inversions, atone or more locations relative to a reference sequence. Variants can bemade for example by site-saturation mutagenesis, scanning mutagenesis,insertional mutagenesis, random mutagenesis, site-directed mutagenesis,and directed-evolution, as well as various other recombinationapproaches. Variant polypeptides may differ from a reference polypeptideby a small number of amino acid residues and may be defined by theirlevel of primary amino acid sequence homology/identity with a referencepolypeptide. In general, related polypeptides may have several essentialamino acids in common (which are sometimes referred to as motif). Theidentity of those essential amino acids can be identified from thealignment of related polypeptides. Mutating of one or more of theessential amino acids may change the properties of the polypeptide suchas substrate specificity, thermostability or change of pH-optimum.Mutating of one or more of the non-essential amino acids may havesmaller effect on the properties of the polypeptide such as substratespecificity, thermostability or change of pH-optimum.

In an embodiment variant polypeptides have at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, or even at least 99% amino acidsequence identity with a reference polypeptide. Methods for determiningpercent identity are known in the art and described herein. Generally,the variants retain the characteristic nature of the referencepolypeptide, but have altered properties in some specific aspects. Forexample, a variant may have a modified pH-optimum, a modified substratebinding ability, a modified resistance to enzymatic degradation or otherdegradation, an increased or decreased activity, a modified temperatureor oxidative stability, but retains its characteristic functionality.Variants further include polypeptides with chemical modifications thatchange the characteristics of a reference polypeptide.

According to one aspect of the invention the polypeptide of theinvention may comprise the amino acid sequence set out in SEQ ID NO: 1,4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43 or 46 or SEQ ID NO:2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44 or 47 or anamino acid sequence that differs in 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or12 amino acids from the amino acid sequence set out in SEQ ID NO: 1, 4,7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43 or 46 or SEQ ID NO: 2,5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44 or 47 and whereinthe polypeptide still has the cellulolytic enhancing activity of thepolypeptide of the invention. The skilled person will appreciate thatthese minor amino acid changes in the polypeptide of the invention maybe present (for example, naturally occurring mutations) or made (forexample, using r-DNA technology) without loss of the function oractivity. In case these mutations are present in a binding domain,active site, or other functional domain of the polypeptide, a propertyof the polypeptide may change (for example its thermostability), but thepolypeptide may keep its cellulolytic enhancing activity. In case amutation is present which is not close to the active site, bindingdomain, or other functional domain, less effect may be expected.

Functional equivalents of a polypeptide according to the invention canalso be identified by screening combinatorial libraries of mutants, e.g.truncation mutants, of the polypeptide of the invention for cellulolyticenhancing activity. In one embodiment a variegated library of variantsis generated by combinatorial mutagenesis at the nucleic acid level.Several techniques are known in the art for screening gene products ofcombinatorial libraries made by point mutations of truncation, and forscreening cDNA libraries for gene products having a selected property.The most widely used techniques, which are amenable to high through-putanalysis, for screening large gene libraries typically include cloningthe gene library into replicable expression vectors, transformingappropriate cells with the resulting library of vectors, and expressingthe combinatorial genes under conditions in which detection of a desiredactivity facilitates isolation of the vector encoding the gene whoseproduct was detected.

In addition to the nucleotide sequences shown in SEQ ID NO: 3, 6, 9, 12,15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45 and 48, it will be apparentfor the person skilled in the art that DNA sequence polymorphisms mayexist within a given population, which may lead to changes in the aminoacid sequence of the polypeptide. Such genetic polymorphisms may existin cells from different populations or within a population due tonatural allelic variation. Allelic variants may also include functionalequivalents. Fragments of a polynucleotide according to the inventionmay also comprise polynucleotides not encoding functional polypeptides.Such polynucleotides may function as probes or primers for a PCRreaction.

With regard to polynucleotides, the terms “variant, “derivative”,“mutant” or “homologue” refer to a polynucleotide that encodes a variantpolypeptide, that has a specified degree of homology/identity with areference polynucleotide, or that hybridizes under stringent conditionsto a reference polynucleotide or the complement thereof. Preferably, avariant polynucleotide has at least 60%, at least 65%, at least 70%, atleast 75%, at least 80%, at least 85%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, or even at least 99% nucleotide sequenceidentity with a reference polynucleotide. Methods for determiningpercent identity are known in the art and described herein.

Homology and identity

The terms “sequence homology” or “sequence identity” are usedinterchangeably herein. For the purpose of this invention, it is definedhere that in order to determine the percentage of sequence homology orsequence identity of two amino acid sequences or of two nucleotidesequences, the sequences are aligned for optimal comparison purposes. Inorder to optimize the alignment between the two sequences, gaps may beintroduced in any of the two sequences that are compared. Such alignmentcan be carried out over the full-length of the sequences being compared.Alternatively, the alignment may be carried out over a shorter length,for example over about 20, about 50, about 100 or more nucleotides oramino acids. The sequence identity is the percentage of identicalmatches between the two sequences over the reported aligned region.

A comparison of sequences and determination of percentage of sequenceidentity between two sequences can be accomplished using a mathematicalalgorithm. The skilled person will be aware of the fact that severaldifferent computer programs are available to align two sequences anddetermine the identity between two sequences (Kruskal, J. B. (1983) Anoverview of sequence comparison. In D. Sankoff and J. B. Kruskal, (ed.),Time warps, string edits and macromolecules: the theory and practice ofsequence comparison, pp. 1-44 Addison Wesley). The percent sequenceidentity between two amino acid sequences or between two nucleotidesequences may be determined using the Needleman and Wunsch algorithm forthe alignment of two sequences. (Needleman, S. B. and Wunsch, C. D.(1970) J. Mol. Biol. 48, 443-453). Both amino acid sequences andnucleotide sequences can be aligned by the algorithm. TheNeedleman-Wunsch algorithm has been implemented in the computer programNEEDLE. For the purpose of this invention, the NEEDLE program from theEMBOSS package was used (version 2.8.0 or higher, EMBOSS: The EuropeanMolecular Biology Open Software Suite (2000) Rice, P. Longden, I. andBleasby, A. Trends in Genetics 16, (6) pp 276-277,emboss.bioinformatics.nl). For amino acid sequences, EBLOSUM62 is usedfor the substitution matrix. For nucleotide sequence, EDNAFULL is used.The optional parameters used are a gap-open penalty of 10 and a gapextension penalty of 0.5. The skilled person will appreciate that allthese different parameters will yield slightly different results butthat the overall percentage identity of two sequences is notsignificantly altered when using different algorithms.

After alignment by the program NEEDLE as described above the percentageof sequence identity between a query sequence and a sequence of theinvention is calculated as follows: Number of corresponding positions inthe alignment showing an identical amino acid or identical nucleotide inboth sequences divided by the total length of the alignment aftersubtraction of the total number of gaps in the alignment. The identitydefined as herein can be obtained from NEEDLE by using the NOBRIEFoption and is labeled in the output of the program as“longest-identity”.

The nucleotide and amino acid sequences of the present invention canfurther be used as a “query sequence” to perform a search againstsequence databases to, for example, identify other family members orrelated sequences. Such searches can be performed using the NBLAST andXBLAST programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol.215:403-10. BLAST nucleotide searches can be performed with the NBLASTprogram, score=100, word length=12 to obtain nucleotide sequenceshomologous to polynucleotides of the invention. BLAST protein searchescan be performed with the XBLAST program, score=50, word length=3 toobtain amino acid sequences homologous to polypeptides of the invention.To obtain gapped alignments for comparison purposes, Gapped BLAST can beutilized as described in Altschul et al., (1997) Nucleic Acids Res.25(17): 3389-3402. When utilizing BLAST and Gapped BLAST programs, thedefault parameters of the respective programs (e.g., XBLAST and NBLAST)can be used.

Compositions

The polypeptide of the invention may be comprised in a composition.Preferably, the composition is enriched in the polypeptide. By“enriched” is meant that the polypeptide in the composition isincreased, for example with at least a factor of 1.1, preferably 1.5,more preferably 2 on protein level compared to the composition withoutthe overexpressed polypeptide of the invention. The composition maycomprise a polypeptide of the present invention as the major enzymaticcomponent, e.g. a mono-component composition. Alternatively, thecomposition may comprise multiple enzymatic activities. The polypeptidecompositions may be prepared in accordance with methods known in the artand may be in the form of a liquid or a dry composition. For instance,the polypeptide composition may be in the form of a granulate or amicrogranulate. The polypeptide to be included in the composition may bestabilized in accordance with methods known in the art. The dosage ofthe composition of the invention and other conditions under which thecomposition is used depend on the ultimate use of the composition.

The invention is concerned with a composition comprising (a) apolypeptide according to the invention, and (b) a cellulase and/or ahemicellulase and/or a pectinase. In an embodiment the cellulase is acellobiohydrolase I, a cellobiohydrolase II, an endo-β-1,4-glucanase, aβ-glucosidase or a β-(1,3)(1,4)-glucanase. In an embodiment thehemicellulase is an endoxylanase, a β-xylosidase, anα-L-arabinofuranosidase, an α-D-glucuronidase, an acetyl-xylan esterase,a feruloyl esterase, a coumaroyl esterase, an α-galactosidase, aβ-galactosidase, a β-mannanase or a β-mannosidase. Of course, thecomposition may also comprise more than one cellulase and/or ahemicellulase and/or a pectinase. For example, two cellulases, twohemicellulases and one pectinase or five cellulases, one hemicelluloseand three pectinases. Any combination is possible. Suitable cellulasesand/or hemicellulases and/or pectinases are described herein.

Polypeptides can be produced by different processes and mixed into anoptimal composition or the compositions can be made directly as amixture by one fermentation.

A composition of the invention may comprise one, two or three or moreclasses of cellulase, for example a polypeptide of the invention, anendo-1,4-β-glucanase (EG), an exo-cellobiohydrolase (CBH) and aβ-glucosidase (BG).

A composition of the invention may comprise a polypeptide which has thesame enzymatic activity, for example cellulolytic enhancing activity, asthat provided by a polypeptide of the invention.

A composition of the invention may comprise a polypeptide which has adifferent type of cellulase activity and/or hemicellulase activityand/or pectinase activity than that provided by a polypeptide of theinvention. For example, a composition of the invention may comprise onetype of cellulase and/or hemicellulase activity and/or pectinaseactivity provided by a polypeptide of the invention and a second type ofcellulase and/or hemicellulase activity and/or pectinase activityprovided by an additional cellulose/hemicellulase/pectinase.

Herein, a cellulase is any polypeptide which is capable of degradingand/or hydrolysing cellulose or enhancing the degradation and/orhydrolysis of cellulose. A polypeptide which is capable of degradingcellulose is a polypeptide which is capable of catalysing the process ofbreaking down cellulose into smaller units, either partially, forexample into cellodextrins, or completely into glucose monomers.Degradation will typically take place by a hydrolysis reaction.

Herein, a hemicellulase is any polypeptide which is capable of degradingand/or hydrolysing hemicellulose or enhancing the degradation and/orhydrolysis of hemicellulose. That is to say, a hemicellulase may becapable of degrading one or more of xylan, glucuronoxylan, arabinoxylan,glucomannan and xyloglucan. A polypeptide which is capable of degradinga hemicellulose is a polypeptide which is capable of catalysing theprocess of breaking down the hemicellulose into smaller polysaccharides,either partially, for example into oligosaccharides, or completely intosugar monomers, for example hexose or pentose sugar monomers. Ahemicellulase may give rise to a mixed population of oligosaccharidesand sugar monomers. Degradation will typically take place by ahydrolysis reaction.

Herein, a pectinase is any polypeptide which is capable of degradingpectin. A polypeptide which is capable of degrading pectin is apolypeptide which is capable of catalysing the process of breaking downpectin into smaller units, either partially, for example intooligosaccharides, or completely into sugar monomers. A pectinaseaccording to the invention may give rise to a mixed population ofoligosaccharides and sugar monomers. Degradation will typically takeplace by a hydrolysis reaction.

The composition may comprise a cellulase and/or a hemicellulase and/or apectinase from Rasamsonia or a source other than Rasamsonia. They may beused together with one or more Rasamsonia enzymes or they may be usedwithout additional Rasamsonia enzymes being present.

For example, the composition of the invention may comprise abeta-glucosidase (BG) from Aspergillus, such as Aspergillus oryzae, suchas the one disclosed in WO 02/095014 or the fusion protein havingbeta-glucosidase activity disclosed in WO 2008/057637, or Aspergillusfumigatus, such as the one disclosed as SEQ ID NO:2 in WO 2005/047499 orSEQ ID NO:5 in WO 2014/130812 or an Aspergillus fumigatusbeta-glucosidase variant, such as one disclosed in WO 2012/044915, suchas one with the following substitutions: F100D, S283G, N456E, F512Y(using SEQ ID NO: 5 in WO 2014/130812 for numbering), or Aspergillusaculeatus, Aspergillus niger or Aspergillus kawachi. In anotherembodiment the beta-glucosidase is derived from Penicillium, such asPenicillium brasilianum disclosed as SEQ ID NO:2 in WO 2007/019442, orfrom Trichoderma, such as Trichoderma reesei, such as ones described inU.S. Pat. Nos. 6,022,725, 6,982,159, 7,045,332, 7,005,289, US2006/0258554 US 2004/0102619. In an embodiment even a bacterialbeta-glucosidase can be used. In another embodiment the beta-glucosidaseis derived from Thielavia terrestris (WO 2011/035029) or Trichophaeasaccata (WO 2007/019442). In an embodiment the enzyme compositioncomprises a beta-glucosidase from Rasamsonia, such as Rasamsoniaemersonii (see WO 2012/000886).

For example, the composition of the invention may comprise anendoglucanase (EG) from Trichoderma, such as Trichoderma reesei; fromHumicola, such as a strain of Humicola insolens; from Aspergillus, suchas Aspergillus aculeatus or Aspergillus kawachii; from Erwinia, such asErwinia carotovara; from Fusarium, such as Fusarium oxysporum; fromThielavia, such as Thielavia terrestris; from Humicola, such as Humicolagrisea var. thermoidea or Humicola insolens; from Melanocarpus, such asMelanocarpus albomyces; from Neurospora, such as Neurospora crassa; fromMyceliophthora, such as Myceliophthora thermophila; from Cladorrhinum,such as Cladorrhinum foecundissimum and/or from Chrysosporium, such as astrain of Chrysosporium lucknowense. In an embodiment the endoglucanaseis from Rasamsonia, such as a strain of Rasamsonia emersonii (see WO01/70998). In an embodiment even a bacterial endoglucanase can be usedincluding, but are not limited to, Acidothermus cellulolyticusendoglucanase (see WO 91/05039; WO 93/15186; U.S. Pat. No. 5,275,944; WO96/02551; U.S. Pat. No. 5,536,655, WO 00/70031, WO 05/093050);Thermobifida fusca endoglucanase III (see WO 05/093050); andThermobifida fusca endoglucanase V (see WO 05/093050).

For example, the composition of the invention may comprise acellobiohydrolase I from Aspergillus, such as Aspergillus fumigatus,such as the Cel7A CBH I disclosed in SEQ ID NO:6 in WO 2011/057140 orSEQ ID NO:6 in WO 2014/130812, or from Trichoderma, such as Trichodermareesei; from Chaetomium, such as Chaetomium thermophilum; fromTalaromyces, such as Talaromyces leycettanus or from Penicillium, suchas Penicillium emersonii. In an embodiment the enzyme compositioncomprises a cellobiohydrolase I from Rasamsonia, such as Rasamsoniaemersonii (see WO 2010/122141).

For example, the composition of the invention may comprise acellobiohydrolase II from Aspergillus, such as Aspergillus fumigatus,such as the one in SEQ ID NO:7 in WO 2014/130812 or from Trichoderma,such as Trichoderma reesei, or from Talaromyces, such as Talaromycesleycettanus, or from Thielavia, such as Thielavia terrestris, such ascellobiohydrolase II CEL6A from Thielavia terrestris. In an embodimentthe enzyme composition comprises a cellobiohydrolase II from Rasamsonia,such as Rasamsonia emersonii (see WO 2011/098580).

For example, the composition of the invention may comprise a polypeptidehaving cellulolytic enhancing activity from Thermoascus, such asThermoascus aurantiacus, such as the one described in WO 2005/074656 asSEQ ID NO:2 and SEQ ID NO: 3 in WO2014/130812 and in WO 2010/065830; orfrom Thielavia, such as Thielavia terrestris, such as the one describedin WO 2005/074647 as SEQ ID NO: 8 or SEQ ID NO:4 in WO2014/130812 and inWO 2008/148131, and WO 2011/035027; or from Aspergillus, such asAspergillus fumigatus, such as the one described in WO 2010/138754 asSEQ ID NO:2 or SEQ ID NO: 3 in WO2014/130812; or from Penicillium, suchas Penicillium emersonii, such as the one disclosed as SEQ ID NO:2 in WO2011/041397 or SEQ ID NO:2 in WO2014/130812. Other suitable polypeptideshaving cellulolytic enhancing activity include, but are not limited to,Trichoderma reesei (see WO 2007/089290), Myceliophthora thermophila (seeWO 2009/085935, WO 2009/085859, WO 2009/085864, WO 2009/085868),Penicillium pinophilum (see WO 2011/005867), Thermoascus sp. (see WO2011/039319), and Thermoascus crustaceous (see WO 2011/041504). In anembodiment, the lytic polysaccharide monooxygenase is from Rasamsonia,e.g. Rasamsonia emersonii (see WO 2012/000892). In one aspect, thepolypeptide having cellulolytic enhancing activity is used in thepresence of a soluble activating divalent metal cation according to WO2008/151043, e.g. manganese sulfate. In one aspect, the polypeptidehaving cellulolytic enhancing activity is used in the presence of adioxy compound, a bicylic compound, a heterocyclic compound, anitrogen-containing compound, a quinone compound, a sulfur-containingcompound, or a liquor obtained from a pretreated cellulosic materialsuch as pretreated corn stover.

Other cellulolytic enzymes that may be comprised in the composition ofthe invention are described in WO 98/13465, WO 98/015619, WO 98/015633,WO 99/06574, WO 99/10481, WO 99/025847, WO 99/031255, WO 2002/101078, WO2003/027306, WO 2003/052054, WO 2003/052055, WO 2003/052056, WO2003/052057, WO 2003/052118, WO 2004/016760, WO 2004/043980, WO2004/048592, WO 2005/001065, WO 2005/028636, WO 2005/093050, WO2005/093073, WO 2006/074005, WO 2006/117432, WO 2007/071818, WO2007/071820, WO 2008/008070, WO 2008/008793, U.S. Pat. Nos. 5,457,046,5,648,263, and 5,686,593, to name just a few.

In addition, examples of xylanases that may be comprised in thecomposition of the invention include, but are not limited to, xylanasesfrom Aspergillus aculeatus (see WO 94/21785), Aspergillus fumigatus (seeWO 2006/078256), Penicillium pinophilum (see WO 2011/041405),Penicillium sp. (see WO 2010/126772), Thielavia terrestris NRRL 8126(see WO 2009/079210), Talaromyces leycettanus, Thermobifida fusca, orTrichophaea saccata GH10 (see WO 2011/057083). In an embodiment theenzyme composition comprises an endoxylanase from Rasamsonia, such asRasamsonia emersonii (see WO 02/24926). Examples of beta-xylosidasesthat may be comprised in the composition of the invention include, butare not limited to, beta-xylosidases from Neurospora crassa, Aspergillusfumigatus and Trichoderma reesei. Examples of acetylxylan esterases thatmay be comprised in the enzyme composition include, but are not limitedto, acetylxylan esterases from Aspergillus aculeatus (see WO2010/108918), Chaetomium globosum, Chaetomium gracile, Humicola insolensDSM 1800 (see WO 2009/073709), Hypocrea jecorina (see WO 2005/001036),Myceliophtera thermophila (see WO 2010/014880), Neurospora crassa,Phaeosphaeria nodorum and Thielavia terrestris NRRL 8126 (see WO2009/042846). In an embodiment the enzyme composition comprises anacetyl xylan esterase from Rasamsonia, such as Rasamsonia emersonii (seeWO 2010/000888). Examples of feruloyl esterases (ferulic acid esterases)that may be comprised in the enzyme composition include, but are notlimited to, feruloyl esterases form Humicola insolens DSM 1800 (see WO2009/076122), Neosartorya fischeri, Neurospora crassa, Penicilliumaurantiogriseum (see WO 2009/127729), and Thielavia terrestris (see WO2010/053838 and WO 2010/065448). Examples of arabinofuranosidases thatmay be comprised in the enzyme composition include, but are not limitedto, arabinofuranosidases from Aspergillus niger, Humicola insolens DSM1800 (see WO 2006/114094 and WO 2009/073383) and M. giganteus (see WO2006/114094). Examples of alpha-glucuronidases that may be comprised inthe enzyme composition include, but are not limited to,alpha-glucuronidases from Aspergillus clavatus, Aspergillus fumigatus,Aspergillus niger, Aspergillus terreus, Humicola insolens (see WO2010/014706), Penicillium aurantiogriseum (see WO 2009/068565) andTrichoderma reesei.

A composition of the current invention may comprise, in addition to oneor more polypeptides of the invention, one, two, three, four classes ormore of cellulase, for example one, two, three or four or all of a lyticpolysaccharide monooxygenase (LPMO), an endoglucanase (EG), one or twoexo-cellobiohydrolases (CBH) and a beta-glucosidase (BG). An enzymecomposition of the current invention may comprise two or more of any ofthese classes of cellulase.

A composition of the current invention may comprise, in addition to oneor more polypeptides of the invention, one type of cellulase activityand/or hemicellulase activity and/or pectinase activity provided by acomposition as described herein and a second type of cellulase activityand/or hemicellulase activity and/or pectinase activity provided by anadditional cellulase/hemicellulase/pectinase.

Accordingly, a composition of the current invention may comprise, inaddition to one or more polypeptides of the invention, any cellulase,for example, a lytic polysaccharide monooxygenase, a cellobiohydrolase,an endo-β-1,4-glucanase, a beta-glucosidase or a β-(1,3)(1,4)-glucanase.

In an embodiment the enzyme composition as described herein comprises apolypeptide according to the invention, an endoglucanase, acellobiohydrolase I, a cellobiohydrolase II, a beta-glucosidase, abeta-xylosidase and an endoxylanase.

As used herein, a cellobiohydrolase (EC 3.2.1.91) is any polypeptidewhich is capable of catalyzing the hydrolysis of 1,4-β-D-glucosidiclinkages in cellulose or cellotetraose, releasing cellobiose from theends of the chains. This enzyme may also be referred to as cellulase1,4-β-cellobiosidase, 1,4-β-cellobiohydrolase, 1,4-β-D-glucancellobiohydrolase, avicelase, exo-1,4-β-D-glucanase,exocellobiohydrolase or exoglucanase.

As used herein, an endo-β-1,4-glucanase (EC 3.2.1.4) is any polypeptidewhich is capable of catalyzing the endohydrolysis of 1,4-β-D-glucosidiclinkages in cellulose, lichenin or cereal β-D-glucans. Such apolypeptide may also be capable of hydrolyzing 1,4-linkages inβ-D-glucans also containing 1,3-linkages. This enzyme may also bereferred to as cellulase, avicelase, β-1,4-endoglucan hydrolase,β-1,4-glucanase, carboxymethyl cellulase, celludextrinase,endo-1,4-β-D-glucanase, endo-1,4-β-D-glucanohydrolase,endo-1,4-β-glucanase or endoglucanase.

As used herein, a beta-glucosidase (EC 3.2.1.21) is any polypeptidewhich is capable of catalysing the hydrolysis of terminal, non-reducingβ-D-glucose residues with release of β-D-glucose. Such a polypeptide mayhave a wide specificity for β-D-glucosides and may also hydrolyze one ormore of the following: a β-D-galactoside, an α-L-arabinoside, aβ-D-xyloside or a β-D-fucoside. This enzyme may also be referred to asamygdalase, β-D-glucoside glucohydrolase, cellobiase or gentobiase.

As used herein, a β-(1,3)(1,4)-glucanase (EC 3.2.1.73) is anypolypeptide which is capable of catalysing the hydrolysis of1,4-β-D-glucosidic linkages in β-D-glucans containing 1,3- and1,4-bonds. Such a polypeptide may act on lichenin and cerealβ-D-glucans, but not on β-D-glucans containing only 1,3- or 1,4-bonds.This enzyme may also be referred to as licheninase, 1,3-1,4-β-D-glucan4-glucanohydrolase, β-glucanase, endo-β-1,3-1,4 glucanase, lichenase ormixed linkage β-glucanase. An alternative for this type of enzyme is EC3.2.1.6, which is described as endo-1,3(4)-beta-glucanase. This type ofenzyme hydrolyses 1,3- or 1,4-linkages in beta-D-glucanse when theglucose residue whose reducing group is involved in the linkage to behydrolysed is itself substituted at C-3. Alternative names includeendo-1,3-beta-glucanase, laminarinase, 1,3-(1,3;1,4)-beta-D-glucan 3 (4)glucanohydrolase. Substrates include laminarin, lichenin and cerealbeta-D-glucans.

A composition of the current invention may comprise any hemicellulase,for example, an endoxylanase, a β-xylosidase, aα-L-arabionofuranosidase, an α-D-glucuronidase, an acetyl xylanesterase, a feruloyl esterase, a coumaroyl esterase, an α-galactosidase,a β-galactosidase, a β-mannanase or a β-mannosidase.

As used herein, an endoxylanase (EC 3.2.1.8) is any polypeptide which iscapable of catalysing the endohydrolysis of 1,4-β-D-xylosidic linkagesin xylans. This enzyme may also be referred to as endo-1,4-β-xylanase or1,4-β-D-xylan xylanohydrolase. An alternative is EC 3.2.1.136, aglucuronoarabinoxylan endoxylanase, an enzyme that is able to hydrolyze1,4 xylosidic linkages in glucuronoarabinoxylans.

As used herein, a β-xylosidase (EC 3.2.1.37) is any polypeptide which iscapable of catalysing the hydrolysis of 1,4-β-D-xylans, to removesuccessive D-xylose residues from the non-reducing termini. Such enzymesmay also hydrolyze xylobiose. This enzyme may also be referred to asxylan 1,4-β-xylosidase, 1,4-β-D-xylan xylohydrolase,exo-1,4-β-xylosidase or xylobiase.

As used herein, an α-L-arabinofuranosidase (EC 3.2.1.55) is anypolypeptide which is capable of acting on α-L-arabinofuranosides,α-L-arabinans containing (1,2) and/or (1,3)- and/or (1,5)-linkages,arabinoxylans and arabinogalactans. This enzyme may also be referred toas α-N-arabinofuranosidase, arabinofuranosidase or arabinosidase.

As used herein, an α-D-glucuronidase (EC 3.2.1.139) is any polypeptidewhich is capable of catalysing a reaction of the following form:alpha-D-glucuronoside+H(2)O=an alcohol+D-glucuronate. This enzyme mayalso be referred to as alpha-glucuronidase or alpha-glucosiduronase.These enzymes may also hydrolyse 4-O-methylated glucoronic acid, whichcan also be present as a substituent in xylans. An alternative is EC3.2.1.131: xylan alpha-1,2-glucuronosidase, which catalyses thehydrolysis of alpha-1,2-(4-O-methyl)glucuronosyl links.

As used herein, an acetyl xylan esterase (EC 3.1.1.72) is anypolypeptide which is capable of catalysing the deacetylation of xylansand xylo-oligosaccharides. Such a polypeptide may catalyze thehydrolysis of acetyl groups from polymeric xylan, acetylated xylose,acetylated glucose, alpha-napthyl acetate or p-nitrophenyl acetate but,typically, not from triacetylglycerol. Such a polypeptide typically doesnot act on acetylated mannan or pectin.

As used herein, a feruloyl esterase (EC 3.1.1.73) is any polypeptidewhich is capable of catalysing a reaction of the form:feruloyl-saccharide+H₂O=ferulate+saccharide. The saccharide may be, forexample, an oligosaccharide or a polysaccharide. It may typicallycatalyse the hydrolysis of the 4-hydroxy-3-methoxycinnamoyl (feruloyl)group from an esterified sugar, which is usually arabinose in ‘natural’substrates. p-nitrophenol acetate and methyl ferulate are typicallypoorer substrates. This enzyme may also be referred to as cinnamoylester hydrolase, ferulic acid esterase or hydroxycinnamoyl esterase. Itmay also be referred to as a hemicellulase accessory enzyme, since itmay help xylanases and pectinases to break down plant cell wallhemicellulose and pectin.

As used herein, a coumaroyl esterase (EC 3.1.1.73) is any polypeptidewhich is capable of catalysing a reaction of the form:coumaroyl-saccharide+H(2)O=coumarate+saccharide. The saccharide may be,for example, an oligosaccharide or a polysaccharide. This enzyme mayalso be referred to as trans-4-coumaroyl esterase, trans-p-coumaroylesterase, p-coumaroyl esterase or p-coumaric acid esterase. This enzymealso falls within EC 3.1.1.73 so may also be referred to as a feruloylesterase.

As used herein, an α-galactosidase (EC 3.2.1.22) is any polypeptidewhich is capable of catalysing the hydrolysis of terminal, non-reducingα-D-galactose residues in α-D-galactosides, including galactoseoligosaccharides, galactomannans, galactans and arabinogalactans. Such apolypeptide may also be capable of hydrolyzing α-D-fucosides. Thisenzyme may also be referred to as melibiase.

As used herein, a β-galactosidase (EC 3.2.1.23) is any polypeptide whichis capable of catalysing the hydrolysis of terminal non-reducingβ-D-galactose residues in β-D-galactosides. Such a polypeptide may alsobe capable of hydrolyzing α-L-arabinosides. This enzyme may also bereferred to as exo-(1->4)-β-D-galactanase or lactase.

As used herein, a β-mannanase (EC 3.2.1.78) is any polypeptide which iscapable of catalysing the random hydrolysis of 1,4-β-D-mannosidiclinkages in mannans, galactomannans and glucomannans. This enzyme mayalso be referred to as mannan endo-1,4-β-mannosidase orendo-1,4-mannanase.

As used herein, a β-mannosidase (EC 3.2.1.25) is any polypeptide whichis capable of catalysing the hydrolysis of terminal, non-reducingβ-D-mannose residues in β-D-mannosides. This enzyme may also be referredto as mannanase or mannase.

A composition of the current invention may comprise any pectinase, forexample an endo-polygalacturonase, a pectin methyl esterase, anendo-galactanase, a beta galactosidase, a pectin acetyl esterase, anendo-pectin lyase, pectate lyase, alpha rhamnosidase, anexo-galacturonase, an expolygalacturonate lyase, a rhamnogalacturonanhydrolase, a rhamnogalacturonan lyase, a rhamnogalacturonan acetylesterase, a rhamnogalacturonan galacturonohydrolase, axylogalacturonase.

As used herein, an endo-polygalacturonase (EC 3.2.1.15) is anypolypeptide which is capable of catalysing the random hydrolysis of1,4-α-D-galactosiduronic linkages in pectate and other galacturonans.This enzyme may also be referred to as polygalacturonase pectindepolymerase, pectinase, endopolygalacturonase, pectolase, pectinhydrolase, pectin polygalacturonase, poly-α-1,4-galacturonideglycanohydrolase, endogalacturonase; endo-D-galacturonase orpoly(1,4-α-D-galacturonide) glycanohydrolase.

As used herein, a pectin methyl esterase (EC 3.1.1.11) is any enzymewhich is capable of catalysing the reaction: pectin+n H₂O=nmethanol+pectate. The enzyme may also been known as pectinesterase,pectin demethoxylase, pectin methoxylase, pectin methylesterase,pectase, pectinoesterase or pectin pectylhydrolase.

As used herein, an endo-galactanase (EC 3.2.1.89) is any enzyme capableof catalysing the endohydrolysis of 1,4-β-D-galactosidic linkages inarabinogalactans. The enzyme may also be known as arabinogalactanendo-1,4β-galactosidase, endo-1,4β-galactanase, galactanase,arabinogalactanase or arabinogalactan 4-β-D-galactanohydrolase.

As used herein, a pectin acetyl esterase is defined herein as any enzymewhich has an acetyl esterase activity which catalyses the deacetylationof the acetyl groups at the hydroxyl groups of GalUA residues of pectin.

As used herein, an endo-pectin lyase (EC 4.2.2.10) is any enzyme capableof catalysing the eliminative cleavage of (1→4)-α-D-galacturonan methylester to give oligosaccharides with4-deoxy-6-O-methyl-α-D-galact-4-enuronosyl groups at their non-reducingends. The enzyme may also be known as pectin lyase, pectintrans-eliminase; endo-pectin lyase, polymethylgalacturonictranseliminase, pectin methyltranseliminase, pectolyase, PL, PNL or PMGLor (1→4)-6-O-methyl-α-D-galacturonan lyase.

As used herein, a pectate lyase (EC 4.2.2.2) is any enzyme capable ofcatalysing the eliminative cleavage of (1→4)-α-D-galacturonan to giveoligosaccharides with 4-deoxy-α-D-galact-4-enuronosyl groups at theirnon-reducing ends. The enzyme may also be known polygalacturonictranseliminase, pectic acid transeliminase, polygalacturonate lyase,endopectin methyltranseliminase, pectate transeliminase,endogalacturonate transeliminase, pectic acid lyase, pectic lyase,α-1,4-D-endopolygalacturonic acid lyase, PGA lyase, PPase-N,endo-α-1,4-polygalacturonic acid lyase, polygalacturonic acid lyase,pectin trans-eliminase, polygalacturonic acid trans-eliminase or(1→4)-α-D-galacturonan lyase.

As used herein, an alpha rhamnosidase (EC 3.2.1.40) is any polypeptidewhich is capable of catalysing the hydrolysis of terminal non-reducingα-L-rhamnose residues in α-L-rhamnosides or alternatively inrhamnogalacturonan. This enzyme may also be known as α-L-rhamnosidase T,α-L-rhamnosidase N or α-L-rhamnoside rhamnohydrolase.

As used herein, exo-galacturonase (EC 3.2.1.82) is any polypeptidecapable of hydrolysis of pectic acid from the non-reducing end,releasing digalacturonate. The enzyme may also be known asexo-poly-α-galacturonosidase, exopolygalacturonosidase orexopolygalacturanosidase.

As used herein, exo-galacturonase (EC 3.2.1.67) is any polypeptidecapable of catalysing:(1,4-α-D-galacturonide)_(n)+H₂O=(1,4-α-D-galacturonide)_(n−1)+D-galacturonate.The enzyme may also be known as galacturan 1,4-α-galacturonidase,exopolygalacturonase, poly(galacturonate) hydrolase,exo-D-galacturonase, exo-D-galacturonanase, exopoly-D-galacturonase orpoly(1,4-α-D-galacturonide) galacturonohydrolase.

As used herein, exopolygalacturonate lyase (EC 4.2.2.9) is anypolypeptide capable of catalysing eliminative cleavage of4-(4-deoxy-α-D-galact-4-enuronosyl)-D-galacturonate from the reducingend of pectate, i.e. de-esterified pectin. This enzyme may be known aspectate disaccharide-lyase, pectate exo-lyase, exopectic acidtranseliminase, exopectate lyase, exopolygalacturonicacid-trans-eliminase, PATE, exo-PATE, exo-PGL or (1→4)-α-D-galacturonanreducing-end-disaccharide-lyase.

As used herein, rhamnogalacturonan hydrolase is any polypeptide which iscapable of hydrolyzing the linkage between galactosyluronic acid andrhamnopyranosyl in an endo-fashion in strictly alternatingrhamnogalacturonan structures, consisting of the disaccharide[(1,2-alpha-L-rhamnoyl-(1,4)-alpha-galactosyluronic acid].

As used herein, rhamnogalacturonan lyase is any polypeptide which is anypolypeptide which is capable of cleaving α-L-Rhap-(1→4)-α-D-GalpAlinkages in an endo-fashion in rhamnogalacturonan by beta-elimination.

As used herein, rhamnogalacturonan acetyl esterase is any polypeptidewhich catalyses the deacetylation of the backbone of alternatingrhamnose and galacturonic acid residues in rhamnogalacturonan.

As used herein, rhamnogalacturonan galacturonohydrolase is anypolypeptide which is capable of hydrolyzing galacturonic acid from thenon-reducing end of strictly alternating rhamnogalacturonan structuresin an exo-fashion.

As used herein, xylogalacturonase is any polypeptide which acts onxylogalacturonan by cleaving the 3-xylose substituted galacturonic acidbackbone in an endo-manner. This enzyme may also be known asxylogalacturonan hydrolase.

As used herein, endo-arabinanase (EC 3.2.1.99) is any polypeptide whichis capable of catalysing endohydrolysis of 1,5-α-arabinofuranosidiclinkages in 1,5-arabinans. The enzyme may also be known asendo-arabinase, arabinan endo-1,5-α-L-arabinosidase,endo-1,5-α-L-arabinanase, endo-α-1,5-arabanase; endo-arabanase or1,5-α-L-arabinan 1,5-α-L-arabinanohydrolase.

A composition of the current invention will typically comprise at leasttwo cellulases, at least one of which may be a polypeptide of theinvention, and optionally at least one hemicellulase and optionally atleast one pectinase. An enzyme composition of the current invention maycomprise a lytic polysaccharide monooxygenases, a cellobiohydrolase, anendoglucanase and/or a beta-glucosidase. Such an enzyme composition mayalso comprise one or more hemicellulases and/or one or more pectinases.

In addition, one or more (for example two, three, four or all) of anamylase, a protease, a lipase, a ligninase, a hexosyltransferase, aglucuronidase, an expansin, a cellulose induced protein or a celluloseintegrating protein or like protein may be present in a composition ofthe current invention.

“Protease” includes enzymes that hydrolyze peptide bonds (peptidases),as well as enzymes that hydrolyze bonds between peptides and othermoieties, such as sugars (glycopeptidases). Many proteases arecharacterized under EC 3.4 and are suitable for use in the processes ofthe current invention. Some specific types of proteases include,cysteine proteases including pepsin, papain and serine proteasesincluding chymotrypsins, carboxypeptidases and metalloendopeptidases.

“Lipase” includes enzymes that hydrolyze lipids, fatty acids, andacylglycerides, including phospoglycerides, lipoproteins,diacylglycerols, and the like. In plants, lipids are used as structuralcomponents to limit water loss and pathogen infection. These lipidsinclude waxes derived from fatty acids, as well as cutin and suberin.

“Ligninase” includes enzymes that can hydrolyze or break down thestructure of lignin polymers. Enzymes that can break down lignin includelignin peroxidases, manganese peroxidases, laccases and feruloylesterases, and other enzymes described in the art known to depolymerizeor otherwise break lignin polymers. Also included are enzymes capable ofhydrolyzing bonds formed between hemicellulosic sugars (notablyarabinose) and lignin. Ligninases include but are not limited to thefollowing group of enzymes: lignin peroxidases (EC 1.11.1.14), manganeseperoxidases (EC 1.11.1.13), laccases (EC 1.10.3.2) and feruloylesterases (EC 3.1.1.73).

“Hexosyltransferase” (2.4.1-) includes enzymes which are capable ofcatalysing a transferase reaction, but which can also catalyze ahydrolysis reaction, for example of cellulose and/or cellulosedegradation products. An example of a hexosyltransferase which may beused in the invention is a β-glucanosyltransferase. Such an enzyme maybe able to catalyze degradation of (1,3)(1,4)glucan and/or celluloseand/or a cellulose degradation product. “Glucuronidase” includes enzymesthat catalyze the hydrolysis of a glucoronoside, for exampleβ-glucuronoside to yield an alcohol. Many glucuronidases have beencharacterized and may be suitable for use in the invention, for exampleβ-glucuronidase (EC 3.2.1.31), hyalurono-glucuronidase (EC 3.2.1.36),glucuronosyl-disulfoglucosamine glucuronidase (3.2.1.56),glycyrrhizinate β-glucuronidase (3.2.1.128) or α-D-glucuronidase (EC3.2.1.139).

A composition of the current invention may comprise an expansin orexpansin-like protein, such as a swollenin (see Salheimo et al., Eur. J.Biochem. 269, 4202-4211, 2002) or a swollenin-like protein.

Expansins are implicated in loosening of the cell wall structure duringplant cell growth. Expansins have been proposed to disrupt hydrogenbonding between cellulose and other cell wall polysaccharides withouthaving hydrolytic activity. In this way, they are thought to allow thesliding of cellulose fibers and enlargement of the cell wall. Swollenin,an expansin-like protein contains an N-terminal Carbohydrate BindingModule Family 1 domain (CBD) and a C-terminal expansin-like domain. Forthe purposes of this invention, an expansin-like protein orswollenin-like protein may comprise one or both of such domains and/ormay disrupt the structure of cell walls (such as disrupting cellulosestructure), optionally without producing detectable amounts of reducingsugars.

A composition of the current invention may comprise a cellulose inducedprotein, for example the polypeptide product of the cip1 or cip2 gene orsimilar genes (see Foreman et al., J. Biol. Chem. 278(34), 31988-31997,2003), a cellulose/cellulosome integrating protein, for example thepolypeptide product of the cipA or cipC gene, or a scaffoldin or ascaffoldin-like protein. Scaffoldins and cellulose integrating proteinsare multi-functional integrating subunits which may organizecellulolytic subunits into a multi-enzyme complex. This is accomplishedby the interaction of two complementary classes of domain, i.e. acohesion domain on scaffoldin and a dockerin domain on each enzymaticunit. The scaffoldin subunit also bears a cellulose-binding module (CBM)that mediates attachment of the cellulosome to its substrate. Ascaffoldin or cellulose integrating protein for the purposes of thisinvention may comprise one or both of such domains.

A composition of the current invention may also comprise a catalase. Theterm “catalase” means a hydrogen-peroxide: hydrogen-peroxideoxidoreductase (EC 1.11.1.6 or EC 1.11.1.21) that catalyzes theconversion of two hydrogen peroxides to oxygen and two waters. Catalaseactivity can be determined by monitoring the degradation of hydrogenperoxide at 240 nm based on the following reaction: 2H₂O₂→2H₂O+O₂. Thereaction is conducted in 50 mM phosphate pH 7.0 at 25° C. with 10.3 mMsubstrate (H₂O₂) and approximately 100 units of enzyme per ml.Absorbance is monitored spectrophotometrically within 16-24 seconds,which should correspond to an absorbance reduction from 0.45 to 0.4. Onecatalase activity unit can be expressed as one micromole of H₂O₂degraded per minute at pH 7.0 and 25° C.

A composition of the current invention may also comprise an amylase. Theterm “amylase” as used herein means enzymes that hydrolyzealpha-1,4-glucosidic linkages in starch, both in amylose andamylopectin, such as alpha-amylase (EC 3.2.1.1), beta-amylase (EC3.2.1.2), glucan 1,4-alpha-glucosidase (EC 3.2.1.3), glucan1,4-alpha-maltotetraohydrolase (EC 3.2.1.60), glucan1,4-alpha-maltohexaosidase (EC 3.2.1.98), glucan1,4-alpha-maltotriohydrolase (EC 3.2.1.116) and glucan1,4-alpha-maltohydrolase (EC 3.2.1.133), and enzymes that hydrolyzealpha-1,6-glucosidic linkages, being the branch-points in amylopectin,such as pullulanase (EC 3.2.1.41) and limit dextinase (EC 3.2.1.142).

A composition of the current invention may be composed of a member ofeach of the classes of enzymes mentioned above, several members of oneenzyme class, or any combination of these enzymes classes or helperproteins (i.e. those proteins mentioned herein which do not haveenzymatic activity per se, but do nevertheless assist in lignocellulosicdegradation).

A composition of the current invention may be composed of enzymes from(1) commercial suppliers; (2) cloned genes expressing enzymes; (3) broth(such as that resulting from growth of a microbial strain in media,wherein the strains secrete proteins and enzymes into the media; (4)cell lysates of strains grown as in (3); and/or (5) plant materialexpressing enzymes. Different enzymes in a composition of the inventionmay be obtained from different sources.

In the uses and processes described herein, the components of thecompositions described above may be provided concomitantly (i.e. as asingle composition per se) or separately or sequentially.

The enzymes can be produced either exogenously in microorganisms,yeasts, fungi, bacteria or plants, then isolated and added, for example,to lignocellulosic material. Alternatively, the enzyme may be producedin a fermentation that uses (pretreated) lignocellulosic material (suchas corn stover or wheat straw) to provide nutrition to an organism thatproduces an enzyme(s). In this manner, plants that produce the enzymesmay themselves serve as a lignocellulosic material and be added intolignocellulosic material.

In an embodiment the composition is a whole fermentation broth. In anembodiment the composition is in the form of a whole fermentation brothof a fungus, preferably Rasamsonia. The whole fermentation broth can beprepared from fermentation of recombinant filamentous fungi. In anembodiment the filamentous fungus is a recombinant filamentous funguscomprising one or more genes which can be homologous or heterologous tothe filamentous fungus. In an embodiment, the filamentous fungus is arecombinant filamentous fungus comprising one or more genes which can behomologous or heterologous to the filamentous fungus wherein the one ormore genes encode enzymes that can degrade a cellulosic substrate. Thewhole fermentation broth may comprise any of the polypeptides describedabove or any combination thereof.

Preferably, the composition is a whole fermentation broth wherein thecells are killed. The whole fermentation broth may contain organicacid(s) (used for killing the cells), killed cells and/or cell debris,and culture medium.

Generally, the filamentous fungi is cultivated in a cell culture mediumsuitable for production of at least a polypeptide of the invention andpreferably one or more enzymes capable of hydrolyzing a cellulosicsubstrate. The cultivation takes place in a suitable nutrient mediumcomprising carbon and nitrogen sources and inorganic salts, usingprocedures known in the art. Suitable culture media, temperature rangesand other conditions suitable for growth and expression of a polypeptideof the invention and, optionally, cellulase and/or hemicellulase and/orpectinase production are known in the art. The whole fermentation brothcan be prepared by growing the filamentous fungi to stationary phase andmaintaining the filamentous fungi under limiting carbon conditions for aperiod of time sufficient to express a polypeptide of the inventionand/or one or more cellulases and/or hemicellulases and/or pectinases.Once enzymes, such as the polypeptide of the invention and/or cellulasesand/or hemicellulases and/or pectinases, are secreted by the filamentousfungi into the fermentation medium, the whole fermentation broth can beused. The whole fermentation broth of the present invention may comprisefilamentous fungi. In some embodiments, the whole fermentation brothcomprises the unfractionated contents of the fermentation materialsderived at the end of the fermentation. Typically, the wholefermentation broth comprises the spent culture medium and cell debrispresent after the filamentous fungi is grown to saturation, incubatedunder carbon-limiting conditions to allow protein synthesis(particularly, expression of cellulases and/or hemicellulases and/orpectinases). In some embodiments, the whole fermentation broth comprisesthe spent cell culture medium, extracellular enzymes and filamentousfungi. In some embodiments, the filamentous fungi present in wholefermentation broth can be lysed, permeabilized, or killed using methodsknown in the art to produce a cell-killed whole fermentation broth. Inan embodiment, the whole fermentation broth is a cell-killed wholefermentation broth, wherein the whole fermentation broth containing thefilamentous fungi cells are lysed or killed. In some embodiments, thecells are killed by lysing the filamentous fungi by chemical and/or pHtreatment to generate the cell-killed whole broth of a fermentation ofthe filamentous fungi. In some embodiments, the cells are killed bylysing the filamentous fungi by chemical and/or pH treatment andadjusting the pH of the cell-killed fermentation mix to a suitable pH.In an embodiment, the whole fermentation broth comprises a first organicacid component comprising at least one 1-5 carbon organic acid and/or asalt thereof and a second organic acid component comprising at least 6or more carbon organic acid and/or a salt thereof. In an embodiment, thefirst organic acid component is acetic acid, formic acid, propionicacid, a salt thereof, or any combination thereof and the second organicacid component is benzoic acid, cyclohexanecarboxylic acid,4-methylvaleric acid, phenylacetic acid, a salt thereof, or anycombination thereof.

The term “whole fermentation broth” as used herein refers to apreparation produced by cellular fermentation that undergoes no orminimal recovery and/or purification. For example, whole fermentationbroths are produced when microbial cultures are grown to saturation,incubated under carbon-limiting conditions to allow protein synthesis(e.g., expression of enzymes by host cells) and secretion into cellculture medium. Typically, the whole fermentation broth isunfractionated and comprises spent cell culture medium, extracellularenzymes, and microbial, preferably non-viable, cells.

If needed, the whole fermentation broth can be fractionated and the oneor more of the fractionated contents can be used. For instance, thekilled cells and/or cell debris can be removed from a whole fermentationbroth to provide a composition that is free of these components.

The whole fermentation broth may further comprise a preservative and/oranti-microbial agent. Such preservatives and/or agents are known in theart.

The whole fermentation broth as described herein is typically a liquid,but may contain insoluble components, such as killed cells, cell debris,culture media components, and/or insoluble enzyme(s). In someembodiments, insoluble components may be removed to provide a clarifiedwhole fermentation broth.

In an embodiment, the whole fermentation broth may be supplemented withone or more enzyme activities that are not expressed endogenously, orexpressed at relatively low level by the filamentous fungi, to improvethe degradation of the cellulosic substrate, for example, to fermentablesugars such as glucose or xylose. The supplemental enzyme(s) can beadded as a supplement to the whole fermentation broth and the enzymesmay be a component of a separate whole fermentation broth, or may bepurified, or minimally recovered and/or purified.

In an embodiment, the whole fermentation broth comprises a wholefermentation broth of a fermentation of recombinant filamentous fungioverexpressing one or more enzymes to improve the degradation of thecellulosic substrate. Alternatively, the whole fermentation broth cancomprise a mixture of a whole fermentation broth of a fermentation of anon-recombinant filamentous fungus and a recombinant filamentous fungusoverexpressing one or more enzymes to improve the degradation of thecellulosic substrate. In an embodiment, the whole fermentation brothcomprises a whole fermentation broth of a fermentation of filamentousfungi overexpressing a polypeptide of the invention. In an embodiment,the whole fermentation broth comprises a whole fermentation broth of afermentation of filamentous fungi overexpressing a beta-glucosidase.Alternatively, the whole fermentation broth for use in the presentmethods and reactive compositions can comprise a mixture of a wholefermentation broth of a fermentation of a non-recombinant filamentousfungus and a whole fermentation broth of a fermentation of recombinantfilamentous fungi overexpressing a polypeptide of the invention and/or abeta-glucosidase.

Polynucleotide Sequence

The invention relates to a polynucleotide, wherein the polynucleotidecomprises a nucleotide sequence that is selected from the groupconsisting of (a) a nucleotide sequence having at least 60% sequenceidentity with the nucleotide sequence of SEQ ID NO: 3, 6, 9, 12, 15, 18,21, 24, 27, 30, 33, 36, 39, 42, 45 and/or 48, (b) a nucleotide sequencewhich hybridises under at least high stringency conditions with thecomplementary strand of SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30,33, 36, 39, 42, 45 and/or 48, (c) a fragment which is at least 100nucleotides in length of a nucleotide sequence as defined in (a) or (b),(d) a nucleotide sequence which is degenerate as a result of the geneticcode to a nucleotide sequence as defined in any one of (a), (b), or (c),and (e) a nucleotide sequence which is the complement of a nucleotidesequence as defined in (a), (b), (c), or (d).

In an embodiment the polynucleotide encodes a polypeptide according tothe invention. In an embodiment the polynucleotide of the presentinvention is isolated.

In an embodiment the polynucleotide of the invention comprises anucleotide sequence having at least 60% sequence identity with thenucleotide sequence of SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30,33, 36, 39, 42, 45 and/or 48. In an embodiment the polynucleotide of theinvention comprises a nucleotide sequence having at least 65% sequenceidentity, at least 70% sequence identity, at least 75% sequenceidentity, at least 76% sequence identity, at least 77% sequenceidentity, at least 78% sequence identity, at least 79% sequenceidentity, at least 80% sequence identity, at least 81% sequenceidentity, at least 82% sequence identity, at least 83% sequenceidentity, at least 84% sequence identity, at least 85% sequenceidentity, at least 86% sequence identity, at least 87% sequenceidentity, at least 88% sequence identity, at least 89% sequenceidentity, at least 90% sequence identity, at least 91% sequenceidentity, at least 92% sequence identity, at least 93% sequenceidentity, at least 94% sequence identity, at least 95% sequenceidentity, at least 96% sequence identity, at least 97% sequenceidentity, at least 98% sequence identity, at least 99% sequenceidentity, with the nucleotide sequence of SEQ ID NO: 3, 6, 9, 12, 15,18, 21, 24, 27, 30, 33, 36, 39, 42, 45 and/or 48. In an embodiment thepolynucleotide of the invention comprises or consists of the nucleotidesequence of SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39,42, 45 or 48.

The invention also relates to a polynucleotide comprising a nucleotidesequence which encodes at least one functional domain of a polypeptideaccording to SEQ ID NO: 1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37,40, 43 and/or 46 or SEQ ID NO: 2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32,35, 38, 41, 44 and/or 47 or a variant thereof, such as a functionalequivalent, or a fragment of either thereof.

A polynucleotide of the present invention, such as a polynucleotidehaving the nucleotide sequence of SEQ ID NO: 3, 6, 9, 12, 15, 18, 21,24, 27, 30, 33, 36, 39, 42, 45 or 48 can be isolated using standardmolecular biology techniques and the sequence information providedherein. For example, using all or a portion of the nucleotide sequenceof SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45 or48 as a hybridization probe, polynucleotides according to the inventioncan be isolated using standard hybridization and cloning techniques(e.g., as described in Sambrook, J., Fritsh, E. F., and Maniatis, T.Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring HarborLaboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,N.Y., 1989).

Moreover, a polynucleotide encompassing all or a portion of SEQ ID NO:3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45 or 48 may beisolated by the polymerase chain reaction (PCR) using syntheticoligonucleotide primers designed based upon the sequence informationcontained in SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39,42, 45 or 48.

A polynucleotide of the invention can be amplified using cDNA, mRNA oralternatively, genomic DNA, as a template and appropriateoligonucleotide primers according to standard PCR amplificationtechniques. The polynucleotide so amplified can be cloned into anappropriate vector and characterized by DNA sequence analysis.

Furthermore, oligonucleotides corresponding to or hybridizing to anucleotide sequence according to the invention can be prepared bystandard synthetic techniques, e.g. using an automated DNA synthesizer.

In a preferred embodiment, an isolated polynucleotide of the inventioncomprises the nucleotide sequence shown in SEQ ID NO: 3, 6, 9, 12, 15,18, 21, 24, 27, 30, 33, 36, 39, 42, 45 or 48.

In another preferred embodiment, an isolated polynucleotide of theinvention comprises a polynucleotide which is the reverse complement ofthe nucleotide sequence shown in SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24,27, 30, 33, 36, 39, 42, 45 or 48.

A polynucleotide which is complementary to a nucleotide sequence is onewhich is sufficiently complementary to the other nucleotide sequencesuch that it can hybridize to the other nucleotide sequence therebyforming a stable duplex. The term “cDNA” (complementary DNA) is definedherein as a DNA molecule which can be prepared by reverse transcriptionfrom a mRNA molecule. cDNA derived from mRNA only contains codingsequences and can be directly translated into the correspondingpolypeptide product. The term “complementary strand” can be usedinterchangeably with the term “complement”. The complement of anucleotide strand can be the complement of a coding strand or thecomplement of a non-coding strand. When referring to double-strandedpolynucleotides, the complement of a polynucleotide encoding apolypeptide refers to the complementary strand of the strand encodingthe amino acid sequence or to any polynucleotide containing the same.

As used herein, the term “hybridization” means the pairing ofsubstantially complementary strands of oligomeric compounds. Onemechanism of pairing involves hydrogen bonding, which may beWatson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, betweencomplementary nucleotide bases (nucleotides) of the strands ofoligomeric compounds. For example, adenine and thymine are complementarynucleic acids which pair through the formation of hydrogen bonds.Hybridization can occur under varying circumstances. “Stringencyhybridization” or “hybridizes under low stringency, medium stringency,high stringency, or very high stringency conditions” is used herein todescribe conditions for hybridization and washing, more specificallyconditions under which an oligomeric compound will hybridize to itstarget sequence, but to a minimal number of other sequences. So, theoligomeric compound will hybridize to the target sequence to adetectably greater degree than to other sequences. Guidance forperforming hybridization reactions can be found in Current Protocols inMolecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6:3.6. Aqueousand non-aqueous methods are described in that reference and either canbe used. Stringency conditions are sequence-dependent and will bedifferent in different circumstances. Generally, stringency conditionsare selected to be about 5° C. lower than the thermal melting point (Tm)for the oligomeric compound at a defined ionic strength and pH. The Tmis the temperature (under defined ionic strength and pH) at which 50% ofan oligomeric compound hybridizes to a perfectly matched probe.Stringency conditions may also be achieved with the addition ofdestabilizing agents such as formamide.

Examples of specific hybridization conditions are as follows: 1) lowstringency hybridization conditions in 6× sodium chloride/sodium citrate(SSC) at about 45° C., followed by two washes in 0.2×SSC, 0.1% SDS atleast at 50° C. (the temperature of the washes can be increased to 55°C. for low stringency conditions); 2) medium stringency hybridizationconditions in 6×SSC at about 45° C., followed by one or more washes in0.2×SSC, 0.1% SDS at 60° C.; 3) high stringency hybridization conditionsin 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC,0.1% SDS at 65° C.; and 4) very high stringency hybridization conditionsare 0.5M sodium phosphate, 7% SDS at 65° C., followed by one or morewashes at 0.2×SSC, 1% SDS at 65° C.

In general, high stringency conditions, such as high hybridizationtemperature and optionally low salt concentrations, permit onlyhybridization between sequences that are highly similar, whereas lowstringency conditions, such as low hybridization temperature andoptionally high salt concentrations, allow hybridization when thesequences are less similar.

One aspect of the invention pertains to isolated polynucleotides thatencode a polypeptide of the invention as well as polynucleotidessufficient for use as hybridization probes to identify polynucleotidesencoding a polypeptide of the invention.

The term “naturally-occurring” as used herein refers to processes,events, or things that occur in their relevant form in nature. Bycontrast, “not naturally-occurring” refers to processes, events, orthings whose existence or form involves the hand of man. Generally, theterm “naturally-occurring” with regard to polypeptides orpolynucleotides can be used interchangeable with the term “wild-type” or“native”. It refers to polypeptide or polynucleotides encoding apolypeptide, having an amino acid sequence or nucleotide sequence,respectively, identical to that found in nature. Naturally occurringpolypeptides include native polypeptides, such as those polypeptidesnaturally expressed or found in a particular host. Naturally occurringpolynucleotides include native polynucleotides such as thosepolynucleotides naturally found in the genome of a particular host.Additionally, a sequence that is wild-type or naturally-occurring mayrefer to a sequence from which a variant or a synthetic sequence isderived.

The polypeptides of the present invention and the polynucleotides of thepresent invention are not naturally-occurring.

As used herein, a “synthetic” molecule is produced by in vitro chemicalor enzymatic synthesis. It includes, but is not limited to,polynucleotides made with optimal codon usage for host organisms ofchoice.

The term “recombinant” when used in reference to a cell, polynucleotide,polypeptide or vector, indicates that the cell, polynucleotide,polypeptide or vector, has been modified by the introduction of aheterologous polynucleotide or polypeptide or the alteration of a nativepolynucleotide or polypeptide, or that the cell is derived from a cellso modified. Thus, for example, recombinant cells expresspolynucleotides that are not found within the native (non-recombinant)form of the cell or express native genes that are otherwise abnormallyexpressed, under expressed or not expressed at all. The term“recombinant” is synonymous with “genetically modified”.

The term “isolated polypeptide” as used herein means a polypeptide thatis removed from at least one component, e.g. other polypeptide material,with which it is naturally associated. Thus, an isolated polypeptide maycontain at most 10%, at most 8%, more preferably at most 6%, morepreferably at most 5%, more preferably at most 4%, more preferably atmost 3%, even more preferably at most 2%, even more preferably at most1% and most preferably at most 0.5% as determined by SDS-PAGE of otherpolypeptide material with which it is natively associated. The isolatedpolypeptide may be free of any other impurities. The isolatedpolypeptide may be at least 50% pure, at least 60% pure, at least 70%pure, at least 75% pure, at least 80% pure, at least 85% pure, at least90% pure, at least 95% pure, at least 96% pure, at least 97% pure, atleast 98% pure, at least 99% pure, at least 99.5% pure, at least 99.9%pure as determined by SDS-PAGE or any other analytical method suitablefor this purpose and known to the person skilled in the art.

An “isolated polynucleotide” or “isolated nucleic acid” is apolynucleotide removed from other polynucleotides with which it isnaturally associated. Thus, an isolated polynucleotide may contain atmost 10%, at most 8%, more preferably at most 6%, more preferably atmost 5%, more preferably at most 4%, more preferably at most 3%, evenmore preferably at most 2%, even more preferably at most 1% and mostpreferably at most 0.5% by weight of other polynucleotide material withwhich it is naturally associated. The isolated polynucleotide may befree of any other impurities. The isolated polynucleotide may be atleast 50% pure, at least 60% pure, at least 70% pure, at least 75% pure,at least 80% pure, at least 85% pure, at least 90% pure, or at least 95%pure, at least 96% pure, at least 97% pure, at least 98% pure, at least99% pure, at least 99.5% pure, at least 99.9% pure by weight.

The term “substantially pure” with regard to polypeptides refers to apolypeptide preparation which contains at the most 50% by weight ofother polypeptide material. The polypeptides disclosed herein arepreferably in a substantially pure form. In particular, it is preferredthat the polypeptides disclosed herein are in “essentially pure form”,i.e. that the polypeptide preparation is essentially free of otherpolypeptide material. Optionally, the polypeptide may also beessentially free of non-polypeptide material such as nucleic acids,lipids, media components, and the like. Herein, the term “substantiallypure polypeptide” is synonymous with the terms “isolated polypeptide”and “polypeptide in isolated form”. The term “substantially pure” withregard to polynucleotide refers to a polynucleotide preparation whichcontains at the most 50% by weight of other polynucleotide material. Thepolynucleotides disclosed herein are preferably in a substantially pureform. In particular, it is preferred that the polynucleotide disclosedherein are in “essentially pure form”, i.e. that the polynucleotidepreparation is essentially free of other polynucleotide material.Optionally, the polynucleotide may also be essentially free ofnon-polynucleotide material such as polypeptides, lipids, mediacomponents, and the like. Herein, the term “substantially purepolynucleotide” is synonymous with the terms “isolated polynucleotide”and “polynucleotide in isolated form”.

The term “nucleic acid” as used in the present invention refers to anucleotide polymer including at least 5 nucleotide units. A nucleic acidrefers to a ribonucleotide polymer (RNA), deoxynucleotide polymer (DNA)or a modified form of either type of nucleic acid or synthetic formthereof or mixed polymers of any of the above. Nucleic acids may includeeither or both naturally-occurring and modified nucleic acids linkedtogether by naturally-occurring and/or non-naturally occurring nucleicacid linkages. The nucleic acid molecules may be modified chemically orbiochemically or may contain non-natural or derivatized nucleic acidbases, as will be readily appreciated by those of skill in the art. Suchmodifications include, for example, labels, methylation, substitution ofone or more of the naturally occurring nucleic acids with an analog,internucleotide modifications such as uncharged linkages (e.g., methylphosphonates, phosphotriesters, phosphoramidates, carbamates, etc.),charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.),pendent moieties (e.g., polypeptides), intercalators (e.g., acridine,psoralen, etc.), chelators, alkylators, and modified linkages (e.g.,alpha anomeric nucleic acids, etc.) The term nucleic acid is alsointended to include any topological conformation, includingsingle-stranded (sense strand and antisense strand), double-stranded,partially duplexed, triplex, hairpinned, circular and padlockedconformations. Also included are synthetic molecules that mimic nucleicacids in their ability to bind to a designated sequence via hydrogenbonding and other chemical interactions. Such molecules are known in theart and include, for example, those in which peptide linkages substitutefor phosphate linkages in the backbone of the molecule. A reference to anucleic acid sequence encompasses its complement unless otherwisespecified. Thus, a reference to a nucleic acid molecule having aparticular sequence should be understood to encompass its complementarystrand, with its complementary sequence. The complementary strand isalso useful, e.g., for antisense therapy, hybridization probes and PCRprimers. The term “nucleic acid”, “nucleic acid molecule” and“polynucleotide” can be used interchangeably herein. The term “nucleicacid sequence” and “nucleotide sequence” can also be usedinterchangeably herein.

A “substitution”, as used herein in relation to polypeptides orpolynucleotides, denotes the replacement of one or more amino acids in apolypeptide sequence or of one or more nucleotides in a nucleotidesequence, respectively, by different amino acids or nucleotides,respectively.

Another embodiment of the invention provides an isolated polynucleotidewhich is antisense to a polynucleotide according to the invention, e.g.the coding strand of a polynucleotide of the present invention. Alsoincluded within the scope of the invention are the complementary strandsof the polynucleotides described herein.

Unless otherwise indicated, all nucleotide sequences determined bysequencing a DNA molecule herein were determined using an automated DNAsequencer and all amino acid sequences of polypeptides encoded by DNAmolecules determined herein were predicted by translation of a DNAsequence determined as above. Therefore, as is known in the art for anyDNA sequence determined by this automated approach, any nucleotidesequence determined herein may contain some errors. Nucleotide sequencesdetermined by automation are typically at least about 90% identical,more typically at least about 95% to at least about 99.9% identical tothe actual nucleotide sequence of the sequenced DNA molecule.

The actual sequence can be more precisely determined by other approachesincluding manual DNA sequencing methods well known in the art. As isalso known in the art, a single insertion or deletion in a determinednucleotide sequence compared to the actual sequence will cause a frameshift in translation of the nucleotide sequence such that the predictedamino acid sequence encoded by a determined nucleotide sequence will becompletely different from the amino acid sequence actually encoded bythe sequenced DNA molecule, beginning at the point of such an insertionor deletion.

The term “deletion” as used herein denotes a change in either amino acidor nucleotide sequence in which one or more amino acids or nucleotides,respectively, are absent as compared to the parent, often thenaturally-occurring, amino acid or nucleotide sequence.

The term “insertion”, also known as the term “addition”, denotes achange in an amino acid or nucleotide sequence resulting in the additionof one or more amino acids or nucleotides, respectively, as compared tothe parent, often the naturally-occurring, amino acid or nucleotidesequence.

A person skilled in the art is capable of identifying such erroneouslyidentified bases and knows how to correct for such errors, for exampleby sequencing the relevant gene.

A polynucleotide according to the invention may comprise only a portionor a fragment of the nucleotide sequence shown in SEQ ID NO: 3, 6, 9,12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45 or 48, for example afragment which can be used as a probe or primer or a fragment encoding aportion of a polypeptide according to the invention.

The probe/primer typically comprises a substantially purifiedoligonucleotide which typically comprises a nucleotide sequence thathybridizes preferably under highly stringent conditions to at least fromabout 12 to about 15, preferably from about 18 to about 20, preferablyfrom about 22 to about 25, more preferably about 30, about 35, about 40,about 45, about 50, about 55, about 60, about 65, or about 75 or moreconsecutive nucleotides of the nucleotide sequence shown in SEQ ID NO:3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45 or 48.

Probes can be used to detect nucleotide sequences encoding the same orhomologous polypeptides, for instance in other organisms. In preferredembodiments, the probe further comprises a label group attached thereto,e.g. the label group can be a radioisotope, a fluorescent compound, anenzyme, or an enzyme cofactor. Such probes can also be used as part of adiagnostic test kit for identifying cells which express a polypeptideaccording to the invention.

The polynucleotides may be synthetic polynucleotides. The syntheticpolynucleotides may be optimized in codon use, preferably according tothe methods described in WO 2006/077258 and/or PCT/EP2007/055943, whichare herein incorporated by reference. PCT/EP2007/055943 addressescodon-pair optimization. Codon-pair optimization is a method wherein thenucleotide sequences encoding a polypeptide have been modified withrespect to their codon usage, in particular the codon pairs that areused, to obtain improved expression of the nucleotide sequence encodingthe polypeptide and/or improved production of the encoded polypeptide.Codon pairs are defined as a set of two subsequent triplets (codons) ina coding sequence. Those skilled in the art will know that the codonusage needs to be adapted depending on the host species, possiblyresulting in variants with significant homology deviation from SEQ IDNO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45 and/or 48,but still encoding the polypeptide of the invention.

The term “expression” includes any step involved in the production ofthe polypeptide including, but not limited to, transcription,post-transcriptional modification, translation, post-translationalmodification, and secretion.

Nucleic Acid Construct

The invention further relates to a nucleic acid construct comprising thepolynucleotide of the present invention. The term “nucleic acidconstruct” is herein referred to as a nucleic acid molecule, eithersingle- or double-stranded, which is isolated from a naturally-occurringgene or which has been modified to contain segments of nucleic acidswhich are combined and juxtaposed in a manner which would not otherwiseexist in nature. The term nucleic acid construct is synonymous with theterm “expression cassette” when the nucleic acid construct contains allthe control sequences required for expression of a coding sequence,wherein said control sequences are operably linked to said codingsequence.

The term “coding sequence” as defined herein is a sequence, which istranscribed into mRNA and translated into a polypeptide. The boundariesof the coding sequence are generally determined by the ATG start codonat the 5′-end of the mRNA and a translation stop codon sequenceterminating the open reading frame at the 3′-end of the mRNA. A codingsequence can include, but is not limited to, DNA, cDNA, and recombinantnucleotide sequences. Preferably, the nucleic acid has high GC content.The GC content herein indicates the number of G and C nucleotides in theconstruct, divided by the total number of nucleotides, expressed in %.The GC content is preferably 56% or more, 57% or more, 58% or more, 59%or more, 60% or more, or in the range of 56-70% or the range of 58-65%.Preferably, the nucleic acid construct comprises a promoter sequence, acoding sequence in operative association with said promoter sequence andcontrol sequences, such as (a) a translational termination sequenceorientated in 5′ towards 3′ direction, and/or (b) a translationalinitiator coding sequence orientated in 5′ towards 3′ direction, and/or(c) a translational initiator sequence

In the context of this invention, the term “translational initiatorcoding sequence” is defined as the nucleotides immediately downstream ofthe initiator or start codon of the open reading frame of a codingsequence. The initiator or start codon encodes for the AA methionine.The initiator codon is typically ATG, but may also be any functionalstart codon such as GTG.

In the context of this invention, the term “translational terminationsequence” is defined as the nucleotides starting from the translationalstop codon at the 3′ end of the open reading frame or nucleotide codingsequence and oriented in 5′ towards 3′ direction.

In the context of this invention, the term “translational initiatorsequence” is defined as the nucleotides immediately upstream of theinitiator or start codon of the open reading frame of a sequence codingfor a polypeptide.

In an embodiment the nucleic acid construct is an expression vector,wherein the polynucleotide according to the invention is operably linkedto at least one control sequence for the expression of thepolynucleotide in a host cell.

An expression vector comprises a polynucleotide coding for apolypeptide, operably linked to the appropriate control sequences (suchas a promoter, and transcriptional and translational stop signals) forexpression and/or translation in vitro or in a host cell. Certainvectors are capable of directing the expression of genes to which theyare operatively linked. Such vectors are referred to herein as“expression vectors”. In general, expression vectors of utility inrecombinant DNA techniques are often in the form of plasmids.

The expression vector may be any vector (e.g. a plasmid or virus), whichcan be conveniently subjected to recombinant DNA procedures and canbring about the expression of the polynucleotide. The choice of thevector will typically depend on the compatibility of the vector with thecell into which the vector is to be introduced. The vectors may belinear or closed circular plasmids. The vector may be an autonomouslyreplicating vector, i.e. a vector which exists as an extra-chromosomalentity, the replication of which is independent of chromosomalreplication, e.g. a plasmid, an extra-chromosomal element, amini-chromosome, or an artificial chromosome. Alternatively, the vectormay be one which, when introduced into the host cell, is integrated intothe genome and replicated together with the chromosome(s) into which ithas been integrated. The integrative cloning vector may integrate atrandom or at a predetermined target locus in the chromosomes of the hostcell.

The vector system may be a single vector or plasmid or two or morevectors or plasmids, which together contain the total DNA to beintroduced into the genome of the host cell, or a transposon.

The vectors preferably contain one or more selectable markers whichpermit easy selection of transformed cells.

Another aspect of the invention pertains to vectors, including cloningand expression vectors, comprising a polynucleotide of the inventionencoding and methods of growing, transforming or transfecting suchvectors in a suitable host cell, for example under conditions in whichexpression of a polypeptide of the invention occurs.

As used herein, the term “vector” refers to a nucleic acid moleculecapable of transporting another nucleic acid to which it has beenlinked. Thus in a further embodiment the invention provides a method ofmaking polynucleotides of the invention by introducing a polynucleotideof the invention into a replicable vector, introducing the vector into acompatible host cell, and growing the host cell under conditions whichbring about replication of the vector. The vector may be recovered fromthe host cell. Suitable host cells are described below.

One type of vector is a “plasmid”, which refers to a circular doublestranded DNA loop into which additional DNA segments can be ligated.Another type of vector is a viral vector, wherein additional DNAsegments can be ligated into the viral genome. The terms “plasmid” and“vector” can be used interchangeably herein as the plasmid is the mostcommonly used form of vector. However, the invention is intended toinclude such other forms of expression vectors, such as cosmids, viralvectors (e.g. replication defective retroviruses, adenoviruses andadeno-associated viruses) and phage vectors which serve equivalentfunctions.

Vectors according to the invention may be used in vitro, for example forthe production of RNA or used to transfect or transform a host cell.

A vector of the invention may comprise two or more, for example three,four or five polynucleotides of the invention, for example foroverexpression.

The recombinant expression vectors of the invention comprise apolynucleotide of the invention in a form suitable for expression of thepolynucleotide in a host cell, which means that the recombinantexpression vector includes one or more regulatory sequences selected onthe basis of the host cells to be used for expression, which is operablylinked to the nucleotide sequence to be expressed.

The term “operably linked”, “operatively linked” or “in operativeassociation” as used herein refers to two or more nucleotide sequenceelements that are physically linked and are in a functional relationshipwith each other. For instance, a promoter is operably linked to a codingsequence, if the promoter is able to initiate or regulate thetranscription or expression of a coding sequence, in which case thecoding sequence should be understood as being “under the control of” thepromoter. Generally, when two nucleotide sequences are operably linked,they will be in the same orientation and usually also in the samereading frame. They usually will be essentially contiguous, althoughthis may not be required.

A vector or nucleic construct for a given host cell may thus comprisethe following elements operably linked to each other in a consecutiveorder from the 5′-end to the 3′-end relative to the coding strand of thesequence encoding the polypeptide of the invention: (1) a promotersequence capable of directing transcription of the nucleotide sequenceencoding the polypeptide in the given host cell, (2) optionally, asignal sequence capable of directing secretion of the polypeptide fromthe given host cell into a culture medium, (3) a nucleotide sequence ofthe invention encoding a mature and preferably active form of thepolypeptide of the invention, and preferably also (4) a transcriptiontermination region (terminator) capable of terminating transcriptiondownstream of the nucleotide sequence encoding the polypeptide of theinvention.

Downstream of the nucleotide sequence according to the invention theremay be a 3′-untranslated region containing one or more transcriptiontermination sites (e.g. a terminator). The terminator can, for example,be native to the nucleotide sequence encoding the polypeptide. However,preferably a yeast terminator is used in yeast host cells and afilamentous fungal terminator is used in filamentous fungal host cells.More preferably, the terminator is endogenous to the host cell (in whichthe nucleotide sequence encoding the polypeptide is to be expressed). Inthe transcribed region, a ribosome binding site for translation may bepresent. The coding portion of the mature transcripts expressed by theconstructs will include a translation initiating AUG at the beginningand a termination codon appropriately positioned at the end of thepolypeptide to be translated.

Enhanced expression of the polynucleotide of the invention may also beachieved by the selection of heterologous regulatory regions, e.g.promoter, secretion leader and/or terminator regions, which may serve toincrease expression and, if desired, secretion levels of the polypeptideof the invention from the expression host and/or to provide for theinducible control of the expression of the polypeptide of the invention.

It will be appreciated by those skilled in the art that the design ofthe expression vector can depend on such factors as the choice of thehost cell to be transformed, the level of expression of the polypeptide,etc.

The vectors, such as expression vectors, of the invention can beintroduced into host cells to produce the polypeptide of the invention.The vectors, such as recombinant expression vectors, of the inventioncan be designed for expression of the polypeptides in prokaryotic oreukaryotic cells.

The recombinant expression vector can also be transcribed and translatedin vitro, for example using T7 promoter regulatory sequences and T7polymerase.

For most filamentous fungi and yeast, the vector or nucleic acidconstruct is preferably integrated in the genome of the host cell inorder to obtain stable transformants. However, for certain yeasts alsosuitable episomal vectors are available into which the expressionconstruct can be incorporated for stable and high-level expression.Examples thereof include vectors derived from the 2p and pKD1 plasmidsof Saccharomyces and Kluyveromyces, respectively, or vectors containingan AMA sequence (e.g. AMA1 from Aspergillus). In case the expressionconstructs are integrated in the host cells genome, the constructs areeither integrated at random loci in the genome or at predeterminedtarget loci using homologous recombination, in which case the targetloci preferably comprise a highly expressed gene.

Accordingly, expression vectors useful in the present invention includechromosomal-, episomal- and virus-derived vectors, e.g. vectors derivedfrom bacterial plasmids, bacteriophage, yeast episome, yeast chromosomalelements, viruses such as baculoviruses, papova viruses, vacciniaviruses, adenoviruses, fowl pox viruses, pseudorabies viruses andretroviruses, and vectors derived from combinations thereof, such asthose derived from plasmid and bacteriophage genetic elements, such ascosmids and phagemids.

The term “control sequence” or “regulatory sequence” can be usedinterchangeably with the term “expression-regulating nucleic acidsequence”. The term as used herein refers to nucleotide sequencesnecessary for and/or affecting the expression of an operably linkedcoding sequence in a particular host organism or in vitro. When twonucleic acid sequences are operably linked, they usually will be in thesame orientation and also in the same reading frame. They usually willbe essentially contiguous, although this may not be required. Theexpression-regulating nucleic acid sequences, such as inter aliaappropriate transcription initiation, termination, promoter, leader,signal peptide, pro-peptide, prepro-peptide, or enhancer sequences;Shine-Delgarno sequence, repressor or activator sequences; efficient RNAprocessing signals such as splicing and polyadenylation signals;sequences that stabilize cytoplasmic mRNA; sequences that enhancetranslation efficiency (e.g. ribosome binding sites); sequences thatenhance protein stability; and when desired, sequences that enhanceprotein secretion, can be any nucleotide sequence showing activity inthe host organism of choice and can be derived from genes encodingproteins, which are either homologous or heterologous to the hostorganism. Each control sequence may be native or foreign to thenucleotide sequence encoding the polypeptide. When desired, the controlsequence may be provided with linkers for the purpose of introducingspecific restriction sites facilitating ligation of the controlsequences with the coding region of the nucleic acid sequence encoding apolypeptide. Control sequences may be optimized to their specificpurpose.

The control sequence may be an appropriate promoter sequence, anucleotide sequence, which is recognized by a host cell for expressionof the nucleotide sequence. The promoter sequence containstranscriptional control sequences, which mediate the expression of thepolypeptide. The promoter may be any nucleotide sequence, which showstranscriptional activity in the cell including mutant, truncated, andhybrid promoters, and may be obtained from genes encoding extracellularor intracellular polypeptides, either homologous or heterologous to thecell.

The term “promoter” is defined herein as a nucleotide sequence thatbinds RNA polymerase and directs the polymerase to the correctdownstream transcriptional start site of a nucleotide sequence encodinga biological compound to initiate transcription. RNA polymeraseeffectively catalyses the assembly of messenger RNA complementary to theappropriate DNA strand of a coding region. The term “promoter” will alsobe understood to include the 5′-non-coding region (between promoter andtranslation start) for translation after transcription into mRNA,cis-acting transcription control elements such as enhancers, and othernucleotide sequences capable of interacting with transcription factors.The promoter may be any appropriate promoter sequence suitable for aeukaryotic or prokaryotic host cell, which shows transcriptionalactivity, including mutant, truncated, and hybrid promoters, and may beobtained from polynucleotides encoding extra-cellular or intracellularpolypeptides either homologous (native) or heterologous (foreign) to thecell.

The promoter may be a constitutive or inducible promoter. Preferably,the promoter is an inducible promoter. More preferably the promoter is acarbohydrate inducible promoter. Carbohydrate inducible promoters areknown in the art. In a preferred embodiment the promoter is suitable infilamentous fungi. Such promoters are known in the art. In a preferredembodiment the promoter is a Rasamsonia promoter. Preferably, thepromoter sequence is from a highly expressed gene. Highly expressedgenes are known in the art.

The promoters used in the host cells of the invention may be modified,if desired, to affect their control characteristics. Suitable promotersin this context include both constitutive and inducible naturalpromoters as well as engineered promoters, which are well known to theperson skilled in the art.

Transcription of the nucleotide sequence encoding the polypeptides ofthe present invention by higher eukaryotes may be increased by insertingan enhancer sequence into the vector. Enhancers are cis-acting elementsof DNA, usually about from 10 to 300 base pairs, that act to increasetranscriptional activity of a promoter in a given host cell type.Examples of suitable enhancers are well known to the person skilled inthe art.

The control sequence may also be a suitable transcription terminatorsequence, a sequence recognized by a host cell to terminatetranscription. The terminator sequence is operably linked to the3′-terminus of the nucleotide sequence encoding the polypeptide. Anyterminator, which is functional in the cell, may be used in the presentinvention. Examples of suitable transcription terminator sequences arewell known to the person skilled in the art.

The control sequence may also include a suitable leader sequence, anon-translated region of a mRNA which is important for translation bythe host cell. The leader sequence is operably linked to the 5′-terminusof the nucleotide sequence encoding the polypeptide. Any leadersequence, which is functional in the cell, may be used in the presentinvention. Examples of suitable leader sequences are well known to theperson skilled in the art.

The control sequence may also be a polyadenylation sequence, a sequencewhich is operably linked to the 3′-terminus of the nucleotide sequenceand which, when transcribed, is recognized by the host cell as a signalto add poly-adenosine residues to transcribed mRNA. Any polyadenylationsequence, which is functional in the cell, may be used in the presentinvention. Examples of suitable polyadenylation sequences are well knownto the person skilled in the art.

When the polypeptide according to the invention is to be secreted fromthe host cell into the cultivation medium, an appropriate signalsequence can be added to the polypeptide in order to direct the de novosynthesized polypeptide to the secretion route of the host cell. Theperson skilled in the art knows to select an appropriate signal sequencefor a specific host. The signal sequence may be native to the host cell,or may be foreign to the host cell. As an example, a signal sequencefrom a protein native to the host cell can be used. Preferably, saidnative protein is a highly secreted protein. Examples of suitable signalsequences are well known to the person skilled in the art.

As an alternative for a signal sequence, the polypeptide of theinvention can be fused to a secreted carrier protein, or part thereof.Such chimeric construct is directed to the secretion route by means ofthe signal sequence of the carrier protein or part thereof. In addition,the carrier protein will provide a stabilizing effect to the polypeptideaccording to the invention and or may enhance solubility. Such carrierprotein may be any protein. Preferably, a highly secreted protein isused as a carrier protein. The carrier protein may be native or foreignto the polypeptide according to the invention. The carrier protein maybe native of may be foreign to the host cell. The carrier protein andpolypeptide according to the invention may contain a specific amino acidmotif to facilitate isolation of the polypeptide. The polypeptideaccording to the invention may be released by a special releasing agent.The releasing agent may be a proteolytic enzyme or a chemical agent.Examples of suitable carrier proteins are well known to the personskilled in the art.

As an alternative for secretion of the polypeptide of the invention intothe medium, the polypeptide of the invention can be fused to alocalisation sequence to target the polypeptide of the invention to adesired cellular compartment, organelle of a cell, or membrane. Suchsequences are known to the person skilled in the art and includeorganelle targeting sequences.

Alternatively, the polypeptide of the invention is fused to anotherprotein that has carbohydrate degrading activity.

Optionally, the polypeptide of the invention is flanked on theC-terminal and/or the N-terminal side by an amino acid motif thatfacilitates identification, isolation and/or purification.

Host Cells

In an embodiment the host cell comprises a polypeptide according to theinvention, a polynucleotide according to the invention or a nucleic acidconstruct according to the invention.

The term “host cell” as used herein means any type of cell that issusceptible to transformation, transfection, transduction or the likewith a polynucleotide according to the invention or a nucleic acidconstruct according to the invention. It encompasses any progeny of aparent cell that is not identical to the parent cell due to mutationsthat occur during replication.

The polypeptides of the present invention can be expressed in bothprokaryotic and eukaryotic cells.

A prokaryotic host cell includes, but is not limited to, a bacterialhost cell. The term “bacterial cell” includes both Gram-negative andGram-positive microorganisms. Examples of bacteria include, but are notlimited to, bacteria belonging to the genus Bacillus (e.g. B. subtilis,B. amyloliquefaciens, B. licheniformis, B. puntis, B. megaterium, B.halodurans, B. pumilus), Acinetobacter, Nocardia, Xanthobacter,Escherichia (e.g. E. coli), Streptomyces, Erwinia, Klebsiella, Serratia(e.g. S. marcessans), Pseudomonas (e.g. P. aeruginosa), Salmonella (e.g.S. typhimurium, S. typhi). Bacteria also include, but are not limitedto, photosynthetic bacteria (e.g. green non-sulfur bacteria (e.g.Choroflexus, Chloronema), green sulfur bacteria (e.g. Chlorobium,Pelodictyon), purple sulfur bacteria (e.g. Chromatium), and purplenon-sulfur bacteria (e.g. Rhodospirillum, Rhodobacter, andRhodomicrobium).

A eukaryotic host cell includes, but is not limited to, a yeast hostcell, a nematode host cell, a fungal host cell, an amoeba host cell, anavian host cell, an amphibian host cell, a reptilian host cell, an algalhost cell, a mammalian host cell and an insect host cell.

Suitable host cells are discussed further in Goeddel, Gene ExpressionTechnology: Methods in Enzymology 185, Academic Press, San Diego, Calif.(1990). Representative examples of appropriate host cells are describedbelow. Appropriate culture mediums and conditions for thebelow-described host cells are known in the art.

In a preferred embodiment the host cells are fungal cells, preferablyfilamentous fungal cells, more preferably Rasamsonia cells, mostpreferred Rasamsonia emersonii cells.

“Filamentous fungi” are herein defined as eukaryotic microorganisms thatinclude all filamentous forms of the subdivision Eumycotina and Oomycota(as defined by Hawksworth et al., 1995). Filamentous fungal strainsinclude, but are not limited to, strains of Acremonium, Aspergillus,Agaricus, Aureobasidium, Cryptococcus, Corynascus, Chrysosporium,Filibasidium, Fusarium, Humicola, Magnaporthe, Monascus, Mucor,Myceliophthora, Mortierella, Neocallimastix, Neurospora, Paecilomyces,Penicillium, Piromyces, Phanerochaete Podospora, Pycnoporus, Rhizopus,Schizophyllum, Sordaria, Talaromyces, Rasamsonia, Thermoascus,Thielavia, Tolypocladium, Trametes and Trichoderma. Preferredfilamentous fungal strains that may serve as host cells belong to thespecies Aspergillus niger, Aspergillus oryzae, Aspergillus fumigatus,Penicillium chrysogenum, Penicillium citrinum, Acremonium chrysogenum,Trichoderma reesei, Rasamsonia emersonii (formerly known as Talaromycesemersonii), Aspergillus sojae, Chrysosporium lucknowense, Myceliophtorathermophyla.

Preferred yeast host cells may be selected from the genera:Saccharomyces (e.g. S. cerevisiae, S. bayanus, S. pastorianus, S.carlsbergensis), Kluyveromyces, Candida (e.g. C. revkaufi, C.pulcherrima, C. tropicalis, C. utilis), Pichia (e.g. P. pastoris),Schizosaccharomyces, Hansenula, Kloeckera, Schwanniomyces, and Yarrowia(e.g. Y. lipolytica (formerly classified as Candida lipolytica)).

Examples of insect cells, include, but are not limited to, Drosophila,Spodoptera and Trichoplusa. Examples of nematode cells, include, but arenot limited to, C. elegans cells. Examples of amphibian cells, include,but are not limited to, Xenopus laevis cells). Examples of mammaliancells, include, but are not limited to, NIH3T3, 293, CHO, COS, VERO,C127, BHK, Per-C6, Bowes melanoma and HeLa cells.

In the context of the present invention the “parent host cell” and the“mutant host cell” may be any type of host cell. The specificembodiments of the mutant host cell are described below. It will beclear to those skilled in the art that embodiments applicable to themutant host cell are as well applicable to the parent host cell, unlessotherwise indicated.

The polynucleotide may be heterologous to the genome of the host cell.The term “heterologous” as used herein refers to nucleotide or aminoacid sequences not naturally occurring in a host cell. In other words,the nucleotide or amino acid sequence is not identical to that naturallyfound in the host cell. As used herein, the term “endogenous” or“homologous” refers to a nucleotide or amino acid sequence naturallyoccurring in a host.

In another embodiment, the invention features host cells, e.g.transformed host cells or recombinant host cells that contain a nucleicacid encompassed by the invention. A “transformed cell” or “recombinantcell” is a cell into which (or into an ancestor of which) has beenintroduced, by means of recombinant DNA techniques, a nucleic acidaccording to the invention.

As used herein, the terms “transformed” or “transgenic” with referenceto a cell mean that the cell has a non-native (heterologous) nucleotidesequence integrated into its genome or has an episomal plasmid that ismaintained through multiple generations. The term is synonymous with theterm “recombinant” or “genetically modified”.

A host cell can be chosen that modulates the expression of the insertedsequences or modifies and processes the gene product in a specific,desired fashion. Such modifications (e.g. glycosylation) and processing(e.g. cleavage) of polypeptide products may facilitate optimalfunctioning of the polypeptides.

Various host cells have characteristic and specific mechanisms forpost-translational processing and modification of polypeptides and geneproducts. Appropriate cell lines or host systems familiar to those ofskill in the art of molecular biology and/or microbiology can be chosento ensure the desired and correct modification and processing of theforeign polypeptide expressed. To this end, eukaryotic host cells thatpossess the cellular machinery for proper processing of the primarytranscript, glycosylation, and phosphorylation of the gene product canbe used. Such host cells are well known in the art.

A host cell as defined herein is an organism suitable for geneticmanipulation and one which may be cultured at cell densities useful forindustrial production of a target product. A suitable organism may be amicroorganism, for example one which may be maintained in a fermentationdevice. A host cell may be a host cell found in nature or a host cellderived from a parent host cell after genetic manipulation or classicalmutagenesis.

According to one embodiment of the invention, when the mutant host cellaccording to the invention is a filamentous fungal host cell, the mutanthost cell may comprise one or more modifications in its genome such thatthe mutant host cell is deficient in the production of at least oneproduct selected from glucoamylase (glaA), acid stable alpha-amylase(amyA), neutral alpha-amylase (amyBI and amyBII), oxalic acid hydrolase(oahA), a toxin, preferably ochratoxin and/or fumonisin, a proteasetranscriptional regulator prtT, PepA, a product encoded by the gene hdfAand/or hdfB, a non-ribosomal peptide synthase npsE if compared to aparent host cell and measured under the same conditions.

Therefore, when the mutant microbial host cell according to theinvention is a filamentous fungal host cell, the host cell may compriseone or more modifications in its genome to result in a deficiency in theproduction of the major extracellular aspartic protease PepA. Forexample, the host cell according to the invention may further comprise adisruption of the pepA gene encoding the major extracellular asparticprotease PepA.

When the mutant microbial host cell according to the invention is afilamentous fungal host cell, the host cell according to the inventionmay additionally comprises one or more modifications in its genome toresult in a deficiency in the production of the product encoded by thehdfA (Ku70) and/or hdfB (Ku80) gene. For example, the host cellaccording to the invention may further comprise a disruption of the hdfAand/or hdfB gene.

When the mutant host cell according to the invention is a filamentousfungal host cell, the host cell according to the invention mayadditionally comprise a modification in its genome which results in thedeficiency in the production of the non-ribosomal peptide synthase npsE.

Host cells according to the invention include plant cells and theinvention therefore extends to transgenic organisms, such as plants andparts thereof, which contain one or more cells of the invention. Thecells may heterologous express the polypeptide of the invention or mayheterologous contain one or more of the polynucleotides of theinvention. The transgenic (or genetically modified) plant may thereforehave inserted (e.g. stably) into its genome a sequence encoding one ormore of the polypeptides of the invention. The transformation of plantcells can be performed using known techniques.

In an embodiment the gene encoding for the endogenous LPMO is deleted ormodified in such a way that the endogenous LPMO polypeptide is no longerproduced by the host cells of the invention. Consequently, the only LPMOcomprised in the host cells may be the polypeptide of the invention.

Polypeptide Production

The invention also relates to a process for producing a polypeptideaccording to the invention, which method comprises the steps of (a)cultivating a host cell according to the invention under conditionsconducive to the production of the polypeptide, and (b) optionally,recovering the polypeptide.

The host cells according to the invention may be cultured usingprocedures known in the art. For each combination of a promoter and ahost cell, culture conditions are available which are conducive to theexpression of the polynucleotide sequence encoding the polypeptide ofthe invention. After reaching the desired cell density or titer of thepolypeptide, the culture is stopped and the polypeptide is recoveredusing known procedures.

The fermentation medium can comprise a known culture medium containing acarbon source, a nitrogen source, and an inorganic nutrient sources.Optionally, an inducer may be included.

The selection of the appropriate medium may be based on the choice ofexpression host and/or based on the regulatory requirements of thenucleic acid construct. Such media are known to those skilled in theart. The medium may, if desired, contain additional components favoringthe transformed host cell over other potentially contaminatingmicroorganisms.

The fermentation can be performed over a period of from about 0.5 toabout 30 days. It may be a batch, continuous or fed-batch process,suitably at a temperature in the range of 0-100° C. or 0-80° C., forexample from 0 to 50° C. and/or at a pH from 2 to 10. Preferredfermentation conditions are a temperature in the range of from 20° C. to45° C. and/or at a pH of from 3 to 9. The appropriate conditions areusually selected based on the choice of the host cell and thepolypeptide to be expressed.

After fermentation, if necessary, the cells can be removed from thefermentation broth by means of centrifugation or filtration. Afterfermentation has stopped or after removal of the cells, the polypeptideof the invention may then be recovered and, if desired, purified andisolated by conventional means.

The polypeptide according to the invention can be recovered and purifiedfrom recombinant host cell cultures by methods known in the art. Mostpreferably, high performance liquid chromatography (“HPLC”) is employedfor purification.

If desired, a host cell as described above may be used to in thepreparation of a polypeptide according to the invention. Such a methodtypically comprises cultivating a host cell (e.g. transformed ortransfected with a nucleic acid construct as described above) underconditions to provide for expression of a coding sequence encoding thepolypeptide, and optionally recovering the expressed polypeptide.Polynucleotides of the invention can be incorporated into a recombinantreplicable vector, e.g. an expression vector. The vector may be used toreplicate the nucleic acid in a compatible host cell. Thus, in a furtherembodiment, the invention provides a method of making a polynucleotideof the invention by introducing a polynucleotide of the invention into areplicable vector, introducing the vector into a compatible host cell,and growing the host cell under conditions which bring about thereplication of the vector. The vector may be recovered from the hostcell.

Preferably, the polypeptide is produced as a secreted protein in whichcase the nucleotide sequence encoding the polypeptide in the expressionconstruct is operably linked to a nucleotide sequence encoding a signalsequence. Preferably, the signal sequence is native (homologous) to thenucleotide sequence encoding the polypeptide. Alternatively, the signalsequence is foreign (heterologous) to the nucleotide sequence encodingthe polypeptide, in which case the signal sequence is preferablyendogenous to the host cell in which the nucleotide sequence accordingto the invention is expressed.

In an embodiment the polypeptides of the present invention may beoverexpressed in a host cell compared to the parent host cell in whichthe polypeptide is not overexpressed. Overexpression of a polypeptide isdefined herein as the expression of the polypeptide which results in anactivity of the polypeptide in the host cell being at least 1.1-, atleast 1.25- or at least 1.5-fold the activity of the polypeptide in theparent host cell wherein the polypeptide is not overexpressed.

Preferably, the activity of the polypeptide is at least 2-fold, morepreferably at least 3-fold, more preferably at least 4-fold, morepreferably at least 5-fold, even more preferably at least 10-fold andmost preferably at least 20-fold the activity of the polypeptide in theparent host cell.

Transformation of the host cell may be conducted by any suitable knownmethods, including electroporation methods, particle bombardment ormicro projectile bombardment, protoplast methods and Agrobacteriummediated transformation (AMT).

In order to enhance the amount of copies of the polynucleotide codingfor the polypeptide or coding for a compound involved in the productionby the cell of the polypeptide in the mutated host cell, multipletransformations of the host cell may be required. In this way, theratios of the different polypeptides produced by the host cell may beinfluenced. Also, an expression vector may comprise multiple expressioncassettes to increase the amount of copies of the polynucleotide(s) tobe transformed.

Another way could be to choose different control sequences for thedifferent polynucleotides, which—depending on the choice—may cause ahigher or a lower production of the desired polypeptide(s).

The host cells transformed with the selectable marker can be selectedbased on the presence of the selectable marker.

For stable transfection of mammalian cells, it is known that, dependingupon the expression vector and transfection technique used, only a smallfraction of cells may integrate the foreign polynucleotide into theirgenome. In order to identify and select these integrants, a gene thatencodes a selectable marker (e.g. resistance to antibiotics) isgenerally introduced into the host cells along with the polynucleotideof interest. Preferred selectable markers include, but are not limitedto, those which confer resistance to drugs or which complement a defectin the host cell. The selectable marker may be introduced into the cellon the expression vector as the expression cassette or may be introducedon a separate expression vector.

Preferred selectable markers include, but are not limited to, thosewhich confer resistance to drugs or which complement a defect in thehost cell. Alternatively, specific selection markers can be used such asauxotrophic markers which require corresponding mutant host cells. In apreferred embodiment the selection marker is deleted from thetransformed host cell after introduction of the expression construct, soas to obtain transformed host cells which are free of selection markergenes.

As indicated, the expression vectors will preferably contain selectablemarkers.

Vectors preferred for use in bacteria are for example disclosed inWO-A1-2004/074468, which are hereby enclosed by reference. Othersuitable vectors will be readily apparent to the skilled artisan.

The invention provides a polypeptide having the amino acid sequenceaccording to SEQ ID NO: 1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37,40, 43 and/or 46 or SEQ ID NO: 2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32,35, 38, 41, 44, and/or 47. The invention also provides an amino acidsequence obtainable by expressing the polynucleotide of SEQ ID NO: 3, 6,9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45 and/or 48 in anappropriate host.

An example of a protein or polypeptide having biological activity in anindustrial application is an enzyme. Enzymes are used in the chemicalindustry and other industrial applications when specific catalysts arerequired. Enzymes in general are limited in the number of reactions theyhave evolved to catalyze and their deactivation at high temperatures. Asa consequence, protein engineering is an active area of research andinvolves attempts to create new enzymes with novel properties, eitherthrough rational design or in vitro evolution. These efforts have begunto be successful, and a few enzymes have now been designed to improveenzymatic reactions. For designing it is essential to have startingsequences from useful microorganisms especially thermophilicmicroorganisms like fungi.

Enzymes can be categorized using their Enzyme Commission number (ECnumber) which is a numerical classification scheme for enzymes, based onthe chemical reactions they catalyze.

Cellulosic Material

Cellulosic materials (also called “biomass” or “feedstock” or“lignocellulosic material” herein) are abundant in nature and have greatvalue as alternative energy source. Second generation biofuels, alsoknown as advanced biofuels, are fuels that can be manufactured fromvarious types of biomass. Biomass can be derived from plant materials,but can also include animal materials. The composition of biomassvaries, the major component is cellulose (in general 35-50%), followedby xylan (a type of hemicellulose, in general 20-35%) and lignin (ingeneral 10-25%), in addition to minor components such as proteins, oilsand ash (or inorganic compounds) that make up the remaining fraction ofbiomass. Biomass contains a variety of carbohydrates. The termcarbohydrate is most common in biochemistry, where it is a synonym ofsaccharide. Carbohydrates (saccharides) are divided into four chemicalgroupings: monosaccharides, disaccharides, oligosaccharides, andpolysaccharides. In general, monosaccharides and disaccharides, whichare smaller (lower molecular weight) carbohydrates, are commonlyreferred to as sugars. The enzymatic conversion (such as hydrolysis) ofpolysaccharides to soluble sugars, for example glucose, gluconic acid,xylose, arabinose, galactose, fructose, mannose, rhamnose, ribose,D-galacturonic acid and other hexoses and pentoses occurs under theaction of different enzymes acting in concert.

A composition of the invention may be tailored in view of the particularfeedstock which is to be used. That is to say, the spectrum ofactivities in a composition of the invention may vary depending on thefeedstock in question.

The enzymes used to hydrolyze the feedstock can be produced eitherexogenously in microorganisms such as yeasts, fungi, bacteria or plants,then isolated and added to the feedstock. Alternatively, the enzymes canbe produced, but not isolated, and a whole fermentation broth, or acombination of enzymes and a whole fermentation broth, can be added tothe feedstock. Alternatively, the whole fermentation broth may betreated to prevent further microbial growth (for example, by heating oraddition of antimicrobial agents), then added to the feedstock. Thewhole fermentation broth may include the organism producing theenzyme(s). Alternatively, the enzyme may be produced in a fermentationthat uses feedstock (such as corn stover) to provide nutrition to anorganism that produces an enzyme(s). In this manner, plants that producethe enzymes may serve as the feedstock and be added to feedstock.

Example of suitable cellulosic materials include, but are not limitedto, virgin biomass and/or non-virgin biomass such as agriculturalbiomass, commercial organics, construction and demolition debris,municipal solid waste, waste paper and yard waste. Common forms ofbiomass include trees, shrubs and grasses, wheat, wheat straw, sugarcane bagasse, corn, corn husks, corn cobs, corn kernel including fiberfrom kernels, distillers dried grains, products and by-products frommilling of grains such as corn, wheat and barley (including wet millingand dry milling) often called “bran or fiber” as well as municipal solidwaste, waste paper and yard waste. The biomass can also be, but is notlimited to, herbaceous material, agricultural residues, forestryresidues, municipal solid wastes, waste paper, and pulp and paper millresidues. “Agricultural biomass” includes branches, bushes, canes, cornand corn husks, energy crops, forests, fruits, flowers, grains, grasses,herbaceous crops, leaves, bark, needles, logs, roots, saplings, shortrotation woody crops, shrubs, switch grasses, trees, vegetables, fruitpeels, vines, sugar beet pulp, wheat middlings, oat hulls, and hard andsoft woods (not including woods with deleterious materials). Inaddition, agricultural biomass includes organic waste materialsgenerated from agricultural processes including farming and forestryactivities, specifically including forestry wood waste. Agriculturalbiomass may be any of the afore-stated singularly or in any combinationor mixture thereof. Further examples of suitable biomass are orchardprimings, chaparral, mill waste, urban wood waste, municipal waste,logging waste, forest thinnings, short-rotation woody crops, industrialwaste, wheat straw, oat straw, rice straw, cane straw, barley straw, ryestraw, flax straw, soy hulls, rice hulls, rice straw, corn gluten feed,oat hulls, sugar cane, corn stover, corn stalks, corn cobs, corn husks,prairie grass, gama grass, foxtail; sugar beet pulp, citrus fruit pulp,seed hulls, cellulosic animal wastes, lawn clippings, cotton, seaweed,trees, shrubs, grasses, wheat, wheat straw, sugar cane bagasse, corn,corn husks, corn hobs, corn kernel, fiber from kernels, products andby-products from wet or dry milling of grains, municipal solid waste,waste paper, yard waste, herbaceous material, agricultural residues,forestry residues, municipal solid waste, waste paper, pulp, paper millresidues, branches, bushes, canes, corn, corn husks, an energy crop,forest, a fruit, a flower, a grain, a grass, a herbaceous crop, a leaf,bark, a needle, a log, a root, a sapling, a shrub, switch grass, a tree,a vegetable, fruit peel, a vine, sugar beet pulp, wheat middlings, oathulls, hard or soft wood, organic waste material generated from anagricultural process, forestry wood waste, or a combination of any twoor more thereof.

Apart from virgin biomass or feedstocks already processed in food andfeed or paper and pulping industries, the biomass/feedstock mayadditionally be pretreated with heat, mechanical and/or chemicalmodification or any combination of such methods in order to enhanceenzymatic degradation.

Pretreatment

Before enzymatic treatment, the feedstock may optionally be pretreatedwith heat, mechanical and/or chemical modification or any combination ofsuch methods in order to enhance the accessibility of the substrate toenzymatic hydrolysis and/or hydrolyse the hemicellulose and/orsolubilize the hemicellulose and/or cellulose and/or lignin, in any wayknown in the art. The pretreatment may comprise exposing the cellulosicmaterial to (hot) water, steam (steam explosion), an acid, a base, asolvent, heat, a peroxide, ozone, mechanical shredding, grinding,milling or rapid depressurization, or a combination of any two or morethereof. This chemical pretreatment is often combined withheat-pretreatment, e.g. between 150 and 220° C. for 1 to 30 minutes.

In an embodiment the cellulosic material is pretreated before and/orduring the enzymatic hydrolysis. Pretreatment methods are known in theart and include, but are not limited to, heat, mechanical, chemicalmodification, biological modification and any combination thereof.Pretreatment is typically performed in order to enhance theaccessibility of the cellulosic material to enzymatic hydrolysis and/orhydrolyse the hemicellulose and/or solubilize the hemicellulose and/orcellulose and/or lignin, in the cellulosic material. In an embodiment,the pretreatment comprises treating the cellulosic material with steamexplosion, hot water treatment or treatment with dilute acid or dilutebase. Examples of pretreatment methods include, but are not limited to,steam treatment (e.g. treatment at 100-260° C., at a pressure of 7-45bar, at neutral pH, for 1-10 minutes), dilute acid treatment (e.g.treatment with 0.1-5% H₂SO₄ and/or SO₂ and/or HNO₃ and/or HCl, inpresence or absence of steam, at 120-200° C., at a pressure of 2-15 bar,at acidic pH, for 2-30 minutes), organosolv treatment (e.g. treatmentwith 1-1.5% H₂SO₄ in presence of organic solvent and steam, at 160-200°C., at a pressure of 7-30 bar, at acidic pH, for 30-60 minutes), limetreatment (e.g. treatment with 0.1-2% NaOH/Ca(OH)2 in the presence ofwater/steam at 60-160° C., at a pressure of 1-10 bar, at alkaline pH,for 60-4800 minutes), ARP treatment (e.g. treatment with 5-15% NH₃, at150-180° C., at a pressure of 9-17 bar, at alkaline pH, for 10-90minutes), AFEX treatment (e.g. treatment with >15% NH₃, at 60-140° C.,at a pressure of 8-20 bar, at alkaline pH, for 5-30 minutes).

Hydrolysis

The invention also relates to a process for degrading cellulosicmaterial, the process comprising the step of contacting the cellulosicmaterial with a polypeptide according to the invention or a compositionaccording to the invention. The degradation may result in the productionof a sugar.

The invention also relates to a process for the treatment of acellulosic material which process comprises the step of contacting thecellulosic material with a polypeptide according to the invention or acomposition according to the invention. The treatment may result in theproduction of a sugar.

The invention also relates to a process for the preparation of a sugarproduct from cellulosic material, comprising the steps of (a) enzymatichydrolysis of the cellulosic material using a polypeptide according tothe invention or a composition according to the invention to obtainenzymatically hydrolysed cellulosic material, and, optionally, recoveryof the enzymatically hydrolysed cellulosic material.

In an embodiment the pH of the above processes is between 3.0 and 6.5,preferably between 3.5 and 5.5, more preferably between 4.0 and 5.0.

After the processes have been performed, the cellulosic material may besubjected to at least one solid/liquid separation. The methods andconditions of solid/liquid separation will depend on the type ofcellulosic material used and are well within the scope of the skilledartisan. Examples include, but are not limited to, centrifugation,cyclonic separation, filtration, decantation, sieving and sedimentation.In a preferred embodiment the solid/liquid separation is performed bycentrifugation or sedimentation. During solid/liquid separation, meansand/or aids for improving the separation may be used.

In an embodiment the cellulosic material is subjected to a pretreatmentstep before the above processes. In an embodiment the cellulosicmaterial is subjected to a washing step before the above processes. Inan embodiment the cellulosic material is subjected to at least onesolid/liquid separation before the above processes. So, beforesubjecting the cellulosic material to any of the above processes, it canbe subjected to at least one solid/liquid separation. The solid/liquidseparation may be done before and/or after the pretreatment step.Suitable methods and conditions for a solid/liquid separation have beendescribed above.

In an embodiment the invention relates to processes wherein theenzymatically hydrolysed cellulosic material is subjected to asolid/liquid separation step followed by a detoxification step and/or aconcentration step.

In the processes according to the present invention cellulosic materialmay be added to the one or more containers. In an embodiment thepolypeptide of the invention or composition of the invention is alreadypresent in the one or more containers before the cellulosic material isadded.

In another embodiment the polypeptide of the invention or composition ofthe invention may be added to the one or more containers. In anembodiment the cellulosic material is already present in the one or morecontainers before the polypeptide of the invention or the composition ofthe invention is added. In an embodiment both the cellulosic materialand the polypeptide of the invention or the composition of the inventionare added simultaneously to the one or more containers. The compositionpresent in the one or more containers may be an aqueous composition.

The above processes may comprise a liquefaction step wherein thecellulosic material is liquefied, and a saccharification step whereinthe liquefied cellulosic material is saccharified. The liquefaction stepis sometimes called presaccharification step. In an embodiment theprocesses comprise at least a liquefaction step wherein the cellulosicmaterial is liquefied in at least a first container, and asaccharification step wherein the liquefied cellulosic material issaccharified in the at least first container and/or in at least a secondcontainer. Saccharification can be done in the same container as theliquefaction (i.e. the at least first container), it can also be done ina separate container (i.e. the at least second container). So, in theprocesses according to the present invention liquefaction andsaccharification may be combined. Alternatively, the liquefaction andsaccharification may be separate steps. Liquefaction andsaccharification may be performed at different temperatures, but mayalso be performed at a single temperature. In an embodiment thetemperature of the liquefaction is higher than the temperature of thesaccharification. Liquefaction is preferably carried out at atemperature of 60-75° C. and saccharification is preferably carried outat a temperature of 50-65° C.

The processes can be performed in one or more containers, but can alsobe performed in one or more tubes or any other continuous system. Thisalso holds true when the above processes comprise a liquefaction stepand a saccharification step. The liquefaction step can be performed inone or more containers, but can also be performed in one or more tubesor any other continuous system and/or the saccharification step can beperformed in one or more containers, but can also be performed in one ormore tubes or any other continuous system. Examples of containers to beused in the present invention include, but are not limited to, fed-batchstirred containers, batch stirred containers, continuous flow stirredcontainers with ultrafiltration, and continuous plug-flow columnreactors. Stirring can be done by one or more impellers, pumps and/orstatic mixers.

The polypeptides or compositions used in the above processes may beadded before and/or during the processes. As indicated above, when thecellulosic material is subjected to a solid/liquid separation before theabove processes, the polypeptides or compositions used in the aboveprocesses may be added before the solid/liquid separation.Alternatively, they may also be added after solid/liquid separation orbefore and after solid/liquid separation. The polypeptides orcompositions may also be added during the above processes. In case theabove processes comprise a liquefaction step and saccharification step,additional polypeptides or compositions may be added during and/or afterthe liquefaction step. The additional polypeptides or compositions maybe added before and/or during the saccharification step. Additionalpolypeptides or compositions may also be added after thesaccharification step.

In an embodiment the total process time is 10 hours or more, 12 hours ormore, 14 hours or more, 16 hours or more, 18 hours or more, 20 hours ormore, 30 hours or more, 40 hours or more, 50 hours or more, 60 hours ormore, 70 hours or more, 80 hours or more, 90 hours or more, 100 hours ormore, 110 hours or more, 120 hours or more, 130 hours or more, 140 hoursor more, 150 hours or more, 160 hours or more, 170 hours or more, 180hours or more, 190 hours or more, 200 hours or more.

In an embodiment, the total process time is 10 to 300 hours, 16 to 275hours, preferably 20 to 250 hours, more preferably 30 to 200 hours, mostpreferably 40 to 150 hours.

The viscosity of the cellulosic material in the one or more containersused for the above processes is kept between 10 and 4000 cP, between 10and 2000 cP, preferably between 10 and 1000 cP.

Incubation of cellulosic material under the above conditions results inrelease or liberation of a substantial amount of the sugars from thecellulosic material. By substantial amount is meant at least 20%, 30%,40%, 50%, 60%, 70%, 80%, 90%, 95% or more of the available sugasr.

In case the processes comprise a liquefaction step and asaccharification step, the viscosity of the cellulosic material in theliquefaction step is kept between 10 and 4000 cP, between 10 and 2000cP, preferably between 10 and 1000 cP and/or the viscosity of thecellulosic material in the saccharification step is kept between 10 and1000 cP, between 10 and 900 cP, preferably between 10 and 800 cP.

The viscosity can be determined with a Brookfield DV III Rheometer atthe temperature used for the above processes.

Significantly, the above processes may be carried out using high levelsof dry matter (of the cellulosic material). In an embodiment the drymatter content at the end of the above processes is 5 wt % or higher, 6wt % or higher, 7 wt % or higher, 8 wt % or higher, 9 wt % or higher, 10wt % or higher, 11 wt % or higher, 12 wt % or higher, 13 wt % or higher,14 wt % or higher, 15 wt % or higher, 16 wt % or higher, 17 wt % orhigher, 18 wt % or higher, 19 wt % or higher, 20 wt % or higher, 21 wt %or higher, 22 wt % or higher, 23 wt % or higher, 24 wt % or higher, 25wt % or higher, 26 wt % or higher, 27 wt % or higher, 28 wt % or higher,29 wt % or higher, 30 wt % or higher, 31 wt % or higher, 32 wt % orhigher, 33 wt % or higher, 34 wt % or higher, 35 wt % or higher, 36 wt %or higher, 37 wt % or higher, 38 wt % or higher or 39 wt % or higher. Inan embodiment the dry matter content at the end of the above processesis between 5 wt %-40 wt %, 6 wt %-40 wt %, 7 wt %-40 wt %, 8 wt %-40 wt%, 9 wt %-40 wt %, 10 wt %-40 wt %, 11 wt %-40 wt %, 12 wt %-40 wt %, 13wt %-40 wt %, 14 wt %-40 wt %, 15 wt %-40 wt %, 16 wt %-40 wt %, 17 wt%-40 wt %, 18 wt %-40 wt %, 19 wt %-40 wt %, 20 wt %-40 wt %, 21 wt %-40wt %, 22 wt %-40 wt %, 23 wt %-40 wt %, 24 wt %-40 wt %, 25 wt %-40 wt%, 26 wt %-40 wt %, 27 wt %-40 wt %, 28 wt %-40 wt %, 29 wt %-40 wt %,30 wt %-40 wt %, 31 wt %-40 wt %, 32 wt %-40 wt %, 33 wt %-40 wt %, 34wt %-40 wt %, 35 wt %-40 wt %, 36 wt %-40 wt %, 37 wt %-40 wt %, 38 wt%-40 wt %, 39 wt %-40 wt %. In a preferred embodiment the dry mattercontent is from 10 wt % to 25 wt %.

In an embodiment the dry matter content at the end of the liquefactionstep of the above processes is 5 wt % or higher, 6 wt % or higher, 7 wt% or higher, 8 wt % or higher, 9 wt % or higher, 10 wt % or higher, 11wt % or higher, 12 wt % or higher, 13 wt % or higher, 14 wt % or higher,15 wt % or higher, 16 wt % or higher, 17 wt % or higher, 18 wt % orhigher, 19 wt % or higher, 20 wt % or higher, 21 wt % or higher, 22 wt %or higher, 23 wt % or higher, 24 wt % or higher, 25 wt % or higher, 26wt % or higher, 27 wt % or higher, 28 wt % or higher, 29 wt % or higher,30 wt % or higher, 31 wt % or higher, 32 wt % or higher, 33 wt % orhigher, 34 wt % or higher, 35 wt % or higher, 36 wt % or higher, 37 wt %or higher, 38 wt % or higher or 39 wt % or higher. In an embodiment thedry matter content at the end of the liquefaction step of the the aboveprocesses is between 5 wt %-40 wt %, 6 wt %-40 wt %, 7 wt %-40 wt %, 8wt %-40 wt %, 9 wt %-40 wt %, 10 wt %-40 wt %, 11 wt %-40 wt %, 12 wt%-40 wt %, 13 wt %-40 wt %, 14 wt %-40 wt %, 15 wt %-40 wt %, 16 wt %-40wt %, 17 wt %-40 wt %, 18 wt %-40 wt %, 19 wt %-40 wt %, 20 wt %-40 wt%, 21 wt %-40 wt %, 22 wt %-40 wt %, 23 wt %-40 wt %, 24 wt %-40 wt %,25 wt %-40 wt %, 26 wt %-40 wt %, 27 wt %-40 wt %, 28 wt %-40 wt %, 29wt %-40 wt %, 30 wt %-40 wt %, 31 wt %-40 wt %, 32 wt %-40 wt %, 33 wt%-40 wt %, 34 wt %-40 wt %, 35 wt %-40 wt %, 36 wt %-40 wt %, 37 wt %-40wt %, 38 wt %-40 wt %, 39 wt %-40 wt %. In a preferred embodiment thedry matter content is from 10 wt % to 25 wt %.

In an embodiment the dry matter content at the end of thesaccharification step of the above processes is 5 wt % or higher, 6 wt %or higher, 7 wt % or higher, 8 wt % or higher, 9 wt % or higher, 10 wt %or higher, 11 wt % or higher, 12 wt % or higher, 13 wt % or higher, 14wt % or higher, 15 wt % or higher, 16 wt % or higher, 17 wt % or higher,18 wt % or higher, 19 wt % or higher, 20 wt % or higher, 21 wt % orhigher, 22 wt % or higher, 23 wt % or higher, 24 wt % or higher, 25 wt %or higher, 26 wt % or higher, 27 wt % or higher, 28 wt % or higher, 29wt % or higher, 30 wt % or higher, 31 wt % or higher, 32 wt % or higher,33 wt % or higher, 34 wt % or higher, 35 wt % or higher, 36 wt % orhigher, 37 wt % or higher, 38 wt % or higher or 39 wt % or higher. In anembodiment the dry matter content at the end of the saccharificationstep of the above processes is between 5 wt %-40 wt %, 6 wt %-40 wt %, 7wt %-40 wt %, 8 wt %-40 wt %, 9 wt %-40 wt %, 10 wt %-40 wt %, 11 wt%-40 wt %, 12 wt %-40 wt %, 13 wt %-40 wt %, 14 wt %-40 wt %, 15 wt %-40wt %, 16 wt %-40 wt %, 17 wt %-40 wt %, 18 wt %-40 wt %, 19 wt %-40 wt%, 20 wt %-40 wt %, 21 wt %-40 wt %, 22 wt %-40 wt %, 23 wt %-40 wt %,24 wt %-40 wt %, 25 wt %-40 wt %, 26 wt %-40 wt %, 27 wt %-40 wt %, 28wt %-40 wt %, 29 wt %-40 wt %, 30 wt %-40 wt %, 31 wt %-40 wt %, 32 wt%-40 wt %, 33 wt %-40 wt %, 34 wt %-40 wt %, 35 wt %-40 wt %, 36 wt %-40wt %, 37 wt %-40 wt %, 38 wt %-40 wt %, 39 wt %-40 wt %. In a preferredembodiment the dry matter content is from 10 wt % to 25 wt %.

In an embodiment oxygen is added during the above processes. In anembodiment oxygen is added during at least a part of the aboveprocesses. Oxygen can be added continuously or discontinuously duringthe above processes. In an embodiment oxygen is added one or more timesduring the above processes. In an embodiment oxygen may be added beforethe above processes, during the addition of cellulosic material to acontainer used for the above processes, during the addition of enzyme toa container used for the above processes, during a part of the aboveprocesses, during the whole processes or any combination thereof. Oxygenis added to the one or more containers used in the above processes.

Oxygen can be added in several forms. For example, oxygen can be addedas oxygen gas, oxygen-enriched gas, such as oxygen-enriched air, or air.Oxygen may also be added by means of in situ oxygen generation. Forexample, oxygen may be generated by electrolysis, oxygen may be producedenzymatically, e.g. by the addition of peroxide, or oxygen may beproduced chemically, e.g. by an oxygen generating system such as KHSO₅.For example, oxygen is produced from peroxide by catalase. The peroxidecan be added in the form of dissolved peroxide or generated by anenzymatic or chemical reaction. In case catalase is used as enzyme toproduce oxygen, catalase present in the enzyme composition for thehydrolysis can be used or catalase can be added for this purpose.

Examples how to add oxygen include, but are not limited to, addition ofoxygen by means of sparging, electrolysis, chemical addition of oxygen,filling the one or more containers used in the the above processes fromthe top (plunging the hydrolysate into the tank and consequentlyintroducing oxygen into the hydrolysate) and addition of oxygen to theheadspace of said one or more containers. When oxygen is added to theheadspace of the container(s), sufficient oxygen necessary for thehydrolysis reaction may be supplied. In general, the amount of oxygenadded to the container(s) can be controlled and/or varied. Restrictionof the oxygen supplied is possible by adding only oxygen during part ofthe hydrolysis time in said container(s). Another option is addingoxygen at a low concentration, for example by using a mixture of air andrecycled air (air leaving the container) or by “diluting” air with aninert gas. Increasing the amount of oxygen added can be achieved byaddition of oxygen during longer periods of the hydrolysis time, byadding the oxygen at a higher concentration or by adding more air.Another way to control the oxygen concentration is to add an oxygenconsumer and/or an oxygen generator. Oxygen can be introduced, forexample blown, into the liquid hydrolysis container contents ofcellulosic material. It can also be blown into the headspace of thecontainer.

In an embodiment oxygen is added to the one or more containers used inthe above processes before and/or during and/or after the addition ofthe cellulosic material to said one or more containers. The oxygen maybe introduced together with the cellulosic material that enters thehydrolysis container(s). The oxygen may be introduced into the materialstream that will enter the container(s) or with part of the container(s)contents that passes an external loop of the container(s).

In an embodiment the container(s) used in the the above processes and/orthe fermentation have a volume of at least 1 m³. Preferably, thecontainers have a volume of at least 1 m³, at least 2 m³, at least 3 m³,at least 4 m³, at least 5 m³, at least 6 m³, at least 7 m³, at least 8m³, at least 9 m³, at least 10 m³, at least 15 m³, at least 20 m³, atleast 25 m³, at least 30 m³, at least 35 m³, at least 40 m³, at least 45m³, at least 50 m³, at least 60 m³, at least 70 m³, at least 75 m³, atleast 80 m³, at least 90 m³, at least 100 m³, at least 200 m³, at least300 m³, at least 400 m³, at least 500 m³, at least 600 m³, at least 700m³, at least 800 m³, at least 900 m³, at least 1000 m³, at least 1500m³, at least 2000 m³, at least 2500 m³. In general, the container(s)will be smaller than 3000 m³ or 5000 m³. In a preferred embodiment thecontainers used in the processes of the invention have a volume of 10 m³to 5000 m³, preferably 50 m³ to 5000 m³. In case several containers areused in the the above processes, they may have the same volume, but alsomay have a different volume. In case the above processes comprise aseparate liquefaction step and saccharification step the container(s)used for the liquefaction step and the container(s) used for thesaccharification step may have the same volume, but also may have adifferent volume.

Hydrolysis and fermentation (see below), separate or simultaneous,include, but are not limited to, separate hydrolysis and fermentation(SHF); simultaneous saccharification and fermentation (SSF);simultaneous saccharification and co-fermentation (SSCF); hybridhydrolysis and fermentation (HHF); separate hydrolysis andco-fermentation (SHCF); hybrid hydrolysis and co-fermentation (HHCF);and direct microbial conversion (DMC), also sometimes calledconsolidated bioprocessing (CBP).

Fermentation

The present invention also relates to a process for producing afermentation product, the process comprising the steps of (a)enzymatically hydrolysing a cellulosic material with a polypeptideaccording to the present invention or a composition according to thepresent invention, (b) fermenting the enzymatically hydrolysedcellulosic material to produce a fermentation product, and (c)optionally, recovering of the fermentation product.

For instance, in the process of the invention a polypeptide according tothe present invention or a composition according to the presentinvention acts on a cellulosic material, so as to convert this complexsubstrate to simple sugars and oligosaccharides for the production offermentation products.

The invention thus also provides a process for the preparation of afermentation product, which method comprises (a) degrading cellulosicmaterial using a process as described herein, and (b) fermentation ofthe resulting material, thereby to prepare a fermentation product. Theprocess for the preparation of a fermentation product may optionallycomprise recovery of the fermentation product.

In an embodiment the fermentation (i.e. step b) is performed in one ormore containers. In an embodiment the fermentation is done by an alcoholproducing microorganism to produce alcohol. The alcohol producingmicroorganism may produce, for example, ethanol. In an embodiment thefermentation is done by an organic acid producing microorganism toproduce an organic acid. The fermentation by an alcohol producingmicroorganism to produce alcohol can be done in the same container(s)wherein the step (a) is performed. Alternatively, the fermentation by analcohol producing microorganism to produce alcohol and the fermentationby an organic acid producing microorganism to produce an organic acidcan be performed in one or more separate containers, but may also bedone in one or more of the same containers.

In an embodiment the fermentation is done by a yeast. In an embodimentthe alcohol producing microorganism and/or the organic acid producingmicroorganism is a yeast. In an embodiment the alcohol producingmicroorganism is able to ferment at least a C5 sugar and at least a C6sugar. In an embodiment the organic acid producing microorganism is ableto ferment at least a C6 sugar. In an embodiment the alcohol producingmicroorganism and the organic acid producing microorganism are differentmicroorganisms. In another embodiment the alcohol producingmicroorganism and the organic acid producing microorganism are the samemicroorganism, i.e. the alcohol producing microorganism is also able toproduce organic acid such as succinic acid.

In a further aspect, the invention thus includes fermentation processesin which a microorganism is used for the fermentation of a carbon sourcecomprising sugar(s), e.g. glucose, L-arabinose and/or xylose. The carbonsource may include any carbohydrate oligo- or polymer comprisingL-arabinose, xylose or glucose units, such as e.g. lignocellulose,xylans, cellulose, starch, arabinan and the like. For release of xyloseor glucose units from such carbohydrates, appropriate carbohydrases(such as xylanases, glucanases, amylases and the like) may be added tothe fermentation medium or may be produced by the modified host cell. Inthe latter case, the modified host cell may be genetically engineered toproduce and excrete such carbohydrases. An additional advantage of usingoligo- or polymeric sources of glucose is that it enables to maintain alow(er) concentration of free glucose during the fermentation, e.g. byusing rate-limiting amounts of the carbohydrases. This, in turn, willprevent repression of systems required for metabolism and transport ofnon-glucose sugars such as xylose. In a preferred process the modifiedhost cell ferments both the L-arabinose (optionally xylose) and glucose,preferably simultaneously in which case preferably a modified host cellis used which is insensitive to glucose repression to prevent diauxicgrowth. In addition to a source of L-arabinose, optionally xylose (andglucose) as carbon source, the fermentation medium will further comprisethe appropriate ingredient required for growth of the modified hostcell. Compositions of fermentation media for growth of microorganismssuch as yeasts or filamentous fungi are well known in the art.

The fermentation time may be shorter than in conventional fermentationat the same conditions, wherein part of the enzymatic hydrolysis stillhas to take part during fermentation. In one embodiment, thefermentation time is 100 hours or less, 90 hours or less, 80 hours orless, 70 hours or less, or 60 hours or less, for a sugar composition of50 g/l glucose and corresponding other sugars from the cellulosicmaterial (e.g. 50 g/l xylose, 35 g/l L-arabinose and 10 g/l galactose).For more dilute sugar compositions, the fermentation time maycorrespondingly be reduced. In an embodiment where the fermentationprocess is one for the production of an alcohol such as ethanol, thefermentation time of the ethanol production step is between 10 and 50hours for ethanol made out of C6 sugars and between 20 and 100 hours forethanol made out of C5 sugars. In an embodiment where the fermentationprocess is one for the production of an organic acid such as succinicacid, the fermentation time of the succinic acid production step isbetween 20 and 70 hours.

The fermentation process may be an aerobic or an anaerobic fermentationprocess. An anaerobic fermentation process is herein defined as afermentation process run in the absence of oxygen or in whichsubstantially no oxygen is consumed, preferably less than 5, 2.5 or 1mmol/L/h, more preferably 0 mmol/L/h is consumed (i.e. oxygenconsumption is not detectable), and wherein organic molecules serve asboth electron donor and electron acceptors. In the absence of oxygen,NADH produced in glycolysis and biomass formation, cannot be oxidised byoxidative phosphorylation. To solve this problem many micro-organismsuse pyruvate or one of its derivatives as an electron and hydrogenacceptor thereby regenerating NAD⁺. Thus, in a preferred anaerobicfermentation process pyruvate is used as an electron (and hydrogenacceptor) and is reduced to fermentation products such as ethanol,lactic acid, 3-hydroxy-propionic acid, acrylic acid, acetic acid,succinic acid, citric acid, malic acid, fumaric acid, an amino acid,1,3-propane-diol, ethylene, glycerol, butanol, a β-lactam antibiotic anda cephalosporin. In a preferred embodiment, the fermentation process isanaerobic. An anaerobic process is advantageous, since it is cheaperthan aerobic processes: less special equipment is needed. Furthermore,anaerobic processes are expected to give a higher product yield thanaerobic processes. Under aerobic conditions, usually the biomass yieldis higher than under anaerobic conditions. As a consequence, usuallyunder aerobic conditions, the expected product yield is lower than underanaerobic conditions.

In another embodiment, the fermentation process is under oxygen-limitedconditions. More preferably, the fermentation process is aerobic andunder oxygen-limited conditions. An oxygen-limited fermentation processis a process in which the oxygen consumption is limited by the oxygentransfer from the gas to the liquid. The degree of oxygen limitation isdetermined by the amount and composition of the ingoing gas flow as wellas the actual mixing/mass transfer properties of the fermentationequipment used. Preferably, in a process under oxygen-limitedconditions, the rate of oxygen consumption is at least 5.5, morepreferably at least 6 and even more preferably at least 7 mmol/L/h.

In an embodiment the alcohol fermentation process is anaerobic, whilethe organic acid fermentation process is aerobic, but done underoxygen-limited conditions.

The fermentation process is preferably run at a temperature that isoptimal for the microorganism used. Thus, for most yeasts or fungalcells, the fermentation process is performed at a temperature which isless than 42° C., preferably 38° C. or lower. For yeast or filamentousfungal host cells, the fermentation process is preferably performed at atemperature which is lower than 35, 33, 30 or 28° C. and at atemperature which is higher than 20, 22, or 25° C. In an embodiment thealcohol fermentation step and the organic acid fermentation step areperformed between 25° C. and 35° C.

In an embodiment of the invention, the fermentations are conducted witha fermenting microorganism. In an embodiment of the invention, thealcohol (e.g. ethanol) fermentations of C5 sugars are conducted with aC5 fermenting microorganism. In an embodiment of the invention, thealcohol (e.g. ethanol) fermentations of C6 sugars are conducted with aC5 fermenting microorganism or a commercial C6 fermenting microorganism.Commercially available yeast suitable for ethanol production include,but are not limited to, BIOFERM™ AFT and XR (NABC—North AmericanBioproducts Corporation, GA, USA), ETHANOL RED™ yeast(Fermentis/Lesaffre, USA), FALI™ (Fleischmann's Yeast, USA), FERMIOL™(DSM Specialties), GERT STRAND™ (Gert Strand AB, Sweden), andSUPERSTART™ and THERMOSACC™ fresh yeast (Ethanol Technology, WI, USA).

In an embodiment propagation of the alcohol producing microorganismand/or the organic acid producing microorganism is performed in one ormore propagation containers. After propagation, the alcohol producingmicroorganism and/or the organic acid producing microorganism may beadded to one or more fermentation containers. Alternatively, thepropagation of the alcohol producing microorganism and/or the organicacid producing microorganism is combined with the fermentation by thealcohol producing microorganism and/or the organic acid producingmicroorganism to produce alcohol and/or organic acid, respectively.

In an embodiment the alcohol producing microorganism is a microorganismthat is able to ferment at least one C5 sugar. Preferably, it also isable to ferment at least one C6 sugar. In an embodiment the inventionrelates to a process for the preparation of ethanol from cellulosicmaterial, comprising the steps of (a) performing a process for thepreparation of a sugar product from cellulosic material as describedabove, (b) fermentation of the enzymatically hydrolysed cellulosicmaterial to produce ethanol; and (c) optionally, recovery of theethanol. The fermentation can be done with a microorganism that is ableto ferment at least one C5 sugar.

In an embodiment the organic acid producing microorganism is amicroorganism that is able to ferment at least one C6 sugar. In anembodiment the invention relates to a process for the preparation ofsuccinic acid from cellulosic material, comprising the steps of (a)performing a process for the preparation of a sugar product fromcellulosic material as described above, (b) fermentation of theenzymatically hydrolysed cellulosic material to produce succinic acid;and (c) optionally, recovery of the succinic acid. The fermentation canbe done with a microorganism that is able to ferment at least one C6sugar.

The alcohol producing microorganisms may be a prokaryotic or eukaryoticorganism. The microorganism used in the process may be a geneticallyengineered microorganism. Examples of suitable alcohol producingorganisms are yeasts, for instance Saccharomyces, e.g. Saccharomycescerevisiae, Saccharomyces pastorianus or Saccharomyces uvarum,Hansenula, Issatchenkia, e.g. Issatchenkia orientalis, Pichia, e.g.Pichia stipites or Pichia pastoris, Kluyveromyces, e.g. Kluyveromycesfagilis, Candida, e.g. Candida pseudotropicalis or Candidaacidothermophilum, Pachysolen, e.g. Pachysolen tannophilus or bacteria,for instance Lactobacillus, e.g. Lactobacillus lactis, Geobacillus,Zymomonas, e.g. Zymomonas mobilis, Clostridium, e.g. Clostridiumphytofermentans, Escherichia, e.g. E. coli, Klebsiella, e.g. Klebsiellaoxytoca. In an embodiment the microorganism that is able to ferment atleast one C5 sugar is a yeast. In an embodiment, the yeast belongs tothe genus Saccharomyces, preferably of the species Saccharomycescerevisiae. The yeast, e.g. Saccharomyces cerevisiae, used in theprocesses according to the present invention is capable of convertinghexose (C6) sugars and pentose (C5) sugars. The yeast, e.g.Saccharomyces cerevisiae, used in the processes according to the presentinvention can anaerobically ferment at least one C6 sugar and at leastone C5 sugar. For example, the yeast is capable of using L-arabinose andxylose in addition to glucose anaerobically. In an embodiment, the yeastis capable of converting L-arabinose into L-ribulose and/or xylulose5-phosphate and/or into a desired fermentation product, for example intoethanol. Organisms, for example Saccharomyces cerevisiae strains, ableto produce ethanol from L-arabinose may be produced by modifying a hostyeast introducing the araA (L-arabinose isomerase), araB(L-ribuloglyoxalate) and araD (L-ribulose-5-P4-epimerase) genes from asuitable source. Such genes may be introduced into a host cell in orderthat it is capable of using arabinose. Such an approach is given isdescribed in WO2003/095627. araA, araB and araD genes from Lactobacillusplantarum may be used and are disclosed in WO2008/041840. The araA genefrom Bacillus subtilis and the araB and araD genes from Escherichia colimay be used and are disclosed in EP1499708. In another embodiment, araA,araB and araD genes may derived from of at least one of the genusClavibacter, Arthrobacter and/or Gramella, in particular one ofClavibacter michiganensis, Arthrobacter aurescens, and/or Gramellaforsetii, as disclosed in WO 2009011591. In an embodiment, the yeast mayalso comprise one or more copies of xylose isomerase gene and/or one ormore copies of xylose reductase and/or xylitol dehydrogenase.

The yeast may comprise one or more genetic modifications to allow theyeast to ferment xylose. Examples of genetic modifications areintroduction of one or more xylA-gene, XYL1 gene and XYL2 gene and/orXKS1-gene; deletion of the aldose reductase (GRE3) gene; overexpressionof PPP-genes TAL1, TKL1, RPE1 and RKI1 to allow the increase of the fluxthrough the pentose phosphate pathway in the cell. Examples ofgenetically engineered yeast are described in EP1468093 and/orWO2006/009434.

An example of a suitable commercial yeast is RN1016 that is a xylose andglucose fermenting Saccharomyces cerevisiae strain from DSM, theNetherlands.

In an embodiment, the fermentation process for the production of ethanolis anaerobic. Anaerobic has already been defined earlier herein. Inanother preferred embodiment, the fermentation process for theproduction of ethanol is aerobic. In another preferred embodiment, thefermentation process for the production of ethanol is underoxygen-limited conditions, more preferably aerobic and underoxygen-limited conditions. Oxygen-limited conditions have already beendefined earlier herein.

The volumetric ethanol productivity is preferably at least 0.5, 1.0,1.5, 2.0, 2.5, 3.0, 5.0 or 10.0 g ethanol per litre per hour. Theethanol yield on L-arabinose and optionally xylose and/or glucose in theprocess preferably is at least 20, 25, 30, 35, 40, 45, 50, 60, 70, 80,90, 95 or 98%. The ethanol yield is herein defined as a percentage ofthe theoretical maximum yield, which, for glucose and L-arabinose andoptionally xylose is 0.51 g ethanol per g glucose or xylose.

In one aspect, the fermentation process leading to the production ofethanol, has several advantages by comparison to known ethanolfermentations processes: anaerobic processes are possible; oxygenlimited conditions are possible; higher ethanol yields and ethanolproduction rates can be obtained; the strain used may be able to useL-arabinose and optionally xylose.

Alternatively to the fermentation processes described above, at leasttwo distinct cells may be used, this means this process is aco-fermentation process. All preferred embodiments of the fermentationprocesses as described above are also preferred embodiments of thisco-fermentation process: identity of the fermentation product, identityof source of L-arabinose and source of xylose, conditions offermentation (aerobic or anaerobic conditions, oxygen-limitedconditions, temperature at which the process is being carried out,productivity of ethanol, yield of ethanol).

The organic acid producing microorganisms may be a prokaryotic oreukaryotic organism. The microorganism used in the process may be agenetically engineered microorganism. Examples of suitable organic acidproducing organisms are yeasts, for instance Saccharomyces, e.g.Saccharomyces cerevisiae; fungi for instance Aspergillus strains, suchas Aspergillus niger and Aspergillus fumigatus, Byssochlamys nivea,Lentinus degener, Paecilomyces varioti and Penicillium viniferum; andbacteria, for instance Anaerobiospirillum succiniciproducens,Actinobacillus succinogenes, Mannhei succiniciproducers MBEL 55E,Escherichia coli, Propionibacterium species, Pectinatus sp., Bacteroidessp., such as Bacteroides amylophilus, Ruminococcus flavefaciens,Prevotella ruminicola, Succcinimonas amylolytica, Succinivibriodextrinisolvens, Wolinella succinogenes, and Cytophaga succinicans. Inan embodiment the organic acid producing microorganism that is able toferment at least one C6 sugar is a yeast. In an embodiment, the yeastbelongs to the genus Saccharomyces, preferably of the speciesSaccharomyces cerevisiae. The yeast, e.g. Saccharomyces cerevisiae, usedin the production processes of organic acid according to the presentinvention is capable of converting hexose (C6) sugars. The yeast, e.g.Saccharomyces cerevisiae, used in the processes according to the presentinvention can anaerobically ferment at least one C6 sugar.

The overall reaction time (or the reaction time of hydrolysis step andfermentation step together) may be reduced. In one embodiment, theoverall reaction time is 300 hours or less, 200 hours or less, 150 hoursor less, 140 hours or less, 130 or less, 120 hours or less, 110 hours orless, 100 hours of less, 90 hours or less, 80 hours or less, 75 hours orless, or about 72 hours at 90% glucose yield. Correspondingly, loweroverall reaction times may be reached at lower glucose yield.

Fermentation products that may be produced by the processes of theinvention can be any substance derived from fermentation. They include,but are not limited to, alcohol (such as arabinitol, butanol, ethanol,glycerol, methanol, 1,3-propanediol, sorbitol, and xylitol); organicacid (such as acetic acid, acetonic acid, adipic acid, ascorbic acid,acrylic acid, citric acid, 2,5-diketo-D-gluconic acid, formic acid,fumaric acid, glucaric acid, gluconic acid, glucuronic acid, glutaricacid, 3-hydroxypropionic acid, itaconic acid, lactic acid, maleic acid,malic acid, malonic acid, oxalic acid, oxaloacetic acid, propionic acid,succinic acid, and xylonic acid); ketones (such as acetone); amino acids(such as aspartic acid, glutamic acid, glycine, lysine, serine,tryptophan, and threonine); alkanes (such as pentane, hexane, heptane,octane, nonane, decane, undecane, and dodecane), cycloalkanes (such ascyclopentane, cyclohexane, cycloheptane, and cyclooctane), alkenes (suchas pentene, hexene, heptene, and octene); and gases (such as methane,hydrogen (H₂), carbon dioxide (CO₂), and carbon monoxide (CO)). Thefermentation product can also be a protein, a vitamin, a pharmaceutical,an animal feed supplement, a specialty chemical, a chemical feedstock, aplastic, a solvent, ethylene, an enzyme, such as a protease, acellulase, an amylase, a glucanase, a lactase, a lipase, a lyase, anoxidoreductase, a transferase or a xylanase. In a preferred embodimentan organic acid and/or an alcohol is prepared in the fermentationprocesses of the present invention. In a preferred embodiment succinicacid and/or ethanol is prepared in the fermentation processes of thepresent invention.

Use of the Polypeptide and Composition of the Invention

The polypeptides and polypeptide compositions according to the inventionmay be used in many different applications. For instance, they may beused to produce fermentable sugars. The fermentable sugars can then, aspart of a biofuel process, be converted into biogas or ethanol, butanol,isobutanol, 2-butanol or other fermentation product. A non-exhaustivelist is given above.

By “fermentable sugars” is meant sugars which can be consumed by amicroorganism or converted by a microorganism into a fermentationproduct.

Alternatively, a polypeptide of the invention or a composition of theinvention may be used in the production of a food product, a detergentcomposition, in the paper and pulp industry, in antibacterialformulations, in pharmaceutical products to name just a few. Some of theuses will be illustrated in more detail below.

In the uses and methods described below, the components of thecompositions described above may be provided concomitantly (i.e. as asingle composition per se) or separately or sequentially.

In principle, a polypeptide of the invention or composition of theinvention may be used in any process which requires the treatment of amaterial which comprises polysaccharide. Thus, a polypeptide orcomposition of the invention may be used in the treatment ofpolysaccharide material. Herein, polysaccharide material is a materialwhich comprises or consists essential of one or, more typically, morethan one polysaccharide.

The invention also provides use of a polypeptide or composition adescribed herein in a method for the preparation of biogas. Biogastypically refers to a gas produced by the biological breakdown oforganic matter, for example cellulosic material, in the absence ofoxygen. Biogas originates from biogenic material and is a type ofbiofuel. One type of biogas is produced by anaerobic digestion orfermentation of biodegradable materials such as biomass, manure orsewage, municipal waste, and energy crops. This type of biogas iscomprised primarily of methane and carbon dioxide. The gas methane canbe combusted or oxidized with oxygen. Air contains 21% oxygen. Thisenergy release allows biogas to be used as a fuel. Biogas can be used asa low-cost fuel in any country for any heating purpose, such as cooking.It can also be utilized in modern waste management facilities where itcan be used to run any type of heat engine, to generate eithermechanical or electrical power. The first step in microbial biogasproduction consists in the enzymatic degradation of polymers and complexsubstrates. Accordingly, the invention provides a method for preparationof a biogas in which a cellulosic substrate is contacted with apolypeptide or composition of the invention, thereby to yieldfermentable material which may be converted into a biogas by anorganism, such as a microorganism. In such a method, a polypeptide orcomposition of the invention may be provided by way of an organism, forexample a microorganism which expresses a polypeptide or composition ofthe invention.

The polypeptides and compositions of the invention may be used in amethod of processing material to degrade or modify the cellulose and/orhemicellulose and/or pectic substance constituents of the material. Suchmethods may be useful in the preparation of a food product. Accordingly,the invention provides a method for preparing a food product whichmethod comprises incorporating a polypeptide or composition of theinvention during preparation of the food product. The invention alsoprovides a method of processing a cellulosic material, which methodcomprises contacting the cellulosic material with a polypeptide orcomposition of the invention to degrade or modify the cellulose in thematerial. The present invention also provides a method for reducing theviscosity, clarity and/or filterability of a cellulosic material, whichmethod comprises contacting the material with a polypeptide orcomposition of the invention in an amount effective in degradingcellulose and/or hemicellulose and/or pectic substances in the material.Cellulosic materials in this respect include, but are not limited to,plant pulp, parts of plants and plant extracts. In the context of thisinvention an extract from a plant material is any substance which can bederived from plant material by extraction (mechanical and/or chemical),processing or by other separation techniques. The extract may be juice,nectar, base or concentrate made thereof. The plant material maycomprise or be derived from vegetables (e.g. carrots, celery, onions,legumes or leguminous plants (soy, soybean, peas)) or fruit (e.g., pomeor seed fruit (apples, pears, quince etc.), grapes, tomatoes, citrus(orange, lemon, lime, mandarin), melons, prunes, cherries, blackcurrants, redcurrants, raspberries, strawberries, cranberries, pineappleand other tropical fruits), trees and parts thereof (e.g. pollen, frompine trees), or cereal (oats, barley, wheat, maize, rice). The material(to be hydrolysed) may also be agricultural residues, such as sugar beetpulp, corn cobs, wheat straw, (ground) nutshells, or recyclablematerials, e.g. (waste) paper. The polypeptides of the invention canthus be used to treat plant material including plant pulp and plantextracts. They may also be used to treat liquid or solid foodstuffs oredible foodstuff ingredients, or be used in the extraction of coffee,plant oils, starch or as a thickener in foods. Typically, thepolypeptides of the invention are used as a composition as describedabove. The composition will generally be added to plant pulp obtainableby, for example mechanical processing such as crushing or milling plantmaterial. Incubation of the composition with the plant will typically becarried out for at time of from 10 minutes to 5 hours. The processingtemperature is preferably from about 10° C. to about 55° C. and one canuse from about 10 g to about 300 g of enzyme per ton of material to betreated. The polypeptides or compositions of the invention may be addedsequentially or at the same time to the plant pulp. Depending on thecomposition of the enzyme preparation the plant material may first bemacerated (e.g. to a pure) or liquefied. Using the polypeptides of theinvention processing parameters such as the yield of the extraction,viscosity of the extract and/or quality of the extract can be improved.Alternatively, or in addition to the above, a polypeptide or compositionof the invention may be added to the raw juice obtained from pressing orliquefying the plant pulp. Treatment of the raw juice will be carriedout in a similar manner to the plant pulp in respect of dosage,temperature and holding time. Again, other enzymes such as thosediscussed previously may be included. Typical incubation conditions areas described above. Once the raw juice has been incubated with thepolypeptides or compositions of the invention, the juice is thencentrifuged or (ultra) filtered to produce the final product. Aftertreatment with the polypeptide or composition of the invention, the(end) product can be heat treated, e.g. at about 100° C. for a time offrom about 1 minute to about 1 hour, under conditions to partially orfully inactivate the polypeptide or composition of the invention. Apolypeptide or composition of the invention may also be used during thepreparation of fruit or vegetable purees. The polypeptide or compositionof the invention may also be used in brewing, wine making, distilling orbaking. It may therefore be used in the preparation of alcoholicbeverages such as wine and beer. For example, it may improve thefilterability or clarity, for example of beers, wort (e.g. containingbarley and/or sorghum malt) or wine. Furthermore, a polypeptide orcomposition of the invention may be used for treatment of brewers spentgrain, i.e. residuals from beer wort production containing barley ormalted barley or other cereals, so as to improve the utilization of theresiduals for e.g. animal feed. A polypeptide or composition of theinvention may assist in the removal of dissolved organic substances frombroth or culture media, for example where distillery waste from organicorigin is bio-converted into microbial biomass. The polypeptide orcomposition of the invention may improve filterability and/or reduceviscosity in glucose syrups, such as from cereals produced byliquefaction (e.g. with α-amylase). In baking, the polypeptide orcomposition of the invention may improve the dough structure, modify itsstickiness or suppleness, improve the loaf volume and/or crumb structureor impart better textural characteristics such as break, shred or crumbquality. The present invention thus relates to methods for preparing adough or a cereal-based food product comprising incorporating into thedough a polypeptide or composition of the present invention. This mayimprove one or more properties of the dough or the cereal-based foodproduct obtained from the dough relative to a dough or a cereal-basedfood product in which the polypeptide or composition is notincorporated. The preparation of the cereal-based food product accordingto the invention further can comprise steps known in the art such asboiling, drying, frying, steaming or baking of the obtained dough.Products that are made from a dough that is boiled are for exampleboiled noodles, dumplings, products that are made from fried dough arefor example doughnuts, beignets, fried noodles, products that are madefor steamed dough are for example steamed buns and steamed noodles,examples of products made from dried dough are pasta and dried noodlesand examples of products made from baked dough are bread, cookies andcake. The term “improved property” is defined herein as any property ofa dough and/or a product obtained from the dough, particularly acereal-based food product, which is improved by the action of thepolypeptide or composition according to the invention relative to adough or product in which the polypeptide or composition according tothe invention is not incorporated. The improved property may include,but is not limited to, increased strength of the dough, increasedelasticity of the dough, increased stability of the dough, improvedmachinability of the dough, improved proofing resistance of the dough,reduced stickiness of the dough, improved extensibility of the dough,increased volume of the cereal-based food product, reduced blistering ofthe cereal-based food product, improved crumb structure of the bakedproduct, improved softness of the cereal-based food product, improvedflavour of the cereal-based food product, improved anti-staling of thecereal-based food product. Improved properties related to pasta andnoodle type of cereal-based products are for example improved firmness,reduced stickiness, improved cohesiveness and reduced cooking loss.Non-starch polysaccharides (NSP) can increase the viscosity of thedigesta which can, in turn, decrease nutrient availability and animalperformance. Adding specific nutrients to feed improves animal digestionand thereby reduces feed costs. Non-starch polysaccharides (NSPs) arealso present in virtually all feed ingredients of plant origin. NSPs arepoorly utilized and can, when solubilized, exert adverse effects ondigestion. Exogenous enzymes can contribute to a better utilization ofthese NSPs and as a consequence reduce any anti-nutritional effects. Apolypeptide or composition of the present invention can be used for thispurpose in cereal-based diets for poultry and, to a lesser extent, forpigs and other species.

A polypeptide or composition of the invention may be used in thedetergent industry, for example for removal from laundry ofcarbohydrate-based stains. A detergent composition may comprise apolypeptide or composition of the invention and, in addition, one ormore of a cellulase, a hemicellulase, a pectinase, a protease, a lipase,a cutinase, an amylase or a carbohydrase. A detergent compositioncomprising a polypeptide or composition of the invention may be in anyconvenient form, for example a paste, a gel, a powder or a liquid. Aliquid detergent may be aqueous, typically containing up to about 70%water and from about 0 to about 30% organic solvent or non-aqueousmaterial. Such a detergent composition may, for example, be formulatedas a hand or machine laundry detergent composition including a laundryadditive composition suitable for pre-treatment of stained fabrics and arinse added fabric softener composition, or be formulated as a detergentcomposition for use in general household hard surface cleaningoperations, or be formulated for hand or machine dish washingoperations. In general, the properties of the polypeptide or compositionof the invention should be compatible with the selected detergent (forexample, pH-optimum, compatibility with other enzymatic and/ornon-enzymatic ingredients, etc.) and the polypeptide or composition ofthe invention should be present in an effective amount. A detergentcomposition may comprise a surfactant, for example an anionic ornon-ionic surfactant, a detergent builder or complexing agent, one ormore polymers, a bleaching system (for example an H₂O₂ source) or anenzyme stabilizer. A detergent composition may also comprise any otherconventional detergent ingredient such as, for example, a conditionerincluding a clay, a foam booster, a sud suppressor, an anti-corrosionagent, a soil-suspending agent, an an-soil redeposition agent, a dye, abactericide, an optical brightener, a hydrotropes, a tarnish inhibitoror a perfume.

A polypeptide or composition of the present invention may be used in thepaper and pulp industry, inter alia in the bleaching process to enhancethe brightness of bleached pulps whereby the amount of chlorine used inthe bleaching stages may be reduced, and to increase the freeness ofpulps in the recycled paper process. Furthermore, a polypeptide orcomposition of the invention may be used for treatment oflignocellulosic pulp so as to improve the bleachability thereof. Therebythe amount of chlorine need to obtain a satisfactory bleaching of thepulp may be reduced.

A polypeptide or composition of the invention may be used in a method ofreducing the rate at which cellulose-containing fabrics become harsh orof reducing the harshness of cellulose-containing fabrics, the methodcomprising treating cellulose-containing fabrics with a polypeptide orcomposition as described above. The present invention further relates toa method providing colour clarification of coloured cellulose-containingfabrics, the method comprising treating coloured cellulose-containingfabrics with a polypeptide or composition as described above, and amethod of providing a localized variation in colour of colouredcellulose-containing fabrics, the method comprising treating colouredcellulose-containing fabrics with a polypeptide or composition asdescribed above. The methods of the invention may be carried out bytreating cellulose-containing fabrics during washing. However, ifdesired, treatment of the fabrics may also be carried out during soakingor rinsing or simply by adding the polypeptide or composition asdescribed above to water in which the fabrics are or will be immersed.

In addition, a polypeptide or composition of the present invention canalso be used in antibacterial formulation as well as in pharmaceuticalproducts such as throat lozenges, toothpastes, and mouthwash.

EMBODIMENTS OF THE INVENTION

-   1. A polypeptide having cellulolytic enhancing activity, wherein the    polypeptide is selected from the group consisting of:    -   (a) a polypeptide comprising an amino acid sequence having at        least 60% sequence identity with the amino acid sequence of SEQ        ID NO: 2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44        and/or 47;    -   (b) a polypeptide encoded by a polynucleotide comprising a        nucleotide sequence having at least 60% sequence identity to the        nucleotide sequence of SEQ ID NO: 3, 6, 9, 12, 15, 18, 21, 24,        27, 30, 33, 36, 39, 42, 45 and/or 48,    -   (c) a polypeptide encoded by a polynucleotide comprising a        nucleotide sequence which hybridises under at least high        stringency conditions with the complementary strand of SEQ ID        NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45        and/or 48, and    -   (d) a fragment of the polypeptide of (a), (b), or (c), that has        cellulolytic enhancing activity.-   2. A polynucleotide, wherein the polynucleotide comprises a    nucleotide sequence that is selected from the group consisting of:    -   (a) a nucleotide sequence having at least 60% sequence identity        with the nucleotide sequence of SEQ ID NO: 3, 6, 9, 12, 15, 18,        21, 24, 27, 30, 33, 36, 39, 42, 45 and/or 48,    -   (b) a nucleotide sequence which hybridises under at least high        stringency conditions with the complementary strand of SEQ ID        NO: 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45        and/or 48,    -   (c) a fragment which is at least 100 nucleotides in length of a        nucleotide sequence as defined in (a) or (b),    -   (d) a nucleotide sequence which is degenerate as a result of the        genetic code to a nucleotide sequence as defined in any one of        (a), (b), or (c), and    -   (e) a nucleotide sequence which is the complement of a        nucleotide sequence as defined in (a), (b), (c), or (d).-   3. A polynucleotide according to embodiment 2, which encodes a    polypeptide according to embodiment 1.-   4. A nucleic acid construct comprising the polynucleotide according    to embodiment 2 or 3.-   5. A nucleic acid construct according to embodiment 4 which is an    expression vector, wherein the polynucleotide according to    embodiment 2 or 3 is operably linked to at least one control    sequence for the expression of the polynucleotide in a host cell.-   6. A host cell comprising a polypeptide according to embodiment 1, a    polynucleotide according to embodiment 2 or 3 or a nucleic acid    construct according to embodiment 4 or 5.-   7. A host cell according to embodiment 6 which is a fungal cell.-   8. A process for producing the polypeptide according to embodiment    1, which process comprises the steps of:    -   (c) cultivating a host cell according to embodiment 6 or 7 under        conditions conducive to the production of the polypeptide, and    -   (d) optionally, recovering the polypeptide.-   9. A composition comprising:    -   (a) a polypeptide according to embodiment 1, and    -   (b) a cellulase and/or a hemicellulase and/or a pectinase.-   10. A composition according to embodiment 9, wherein the cellulase    is a cellobiohydrolase I, a cellobiohydrolase II, an    endo-β-1,4-glucanase, a β-glucosidase or a β-(1,3)(1,4)-glucanase.-   11. A composition according to embodiment 9 or 10, wherein the    hemicellulase is an endoxylanase, a β-xylosidase, an    α-L-arabinofuranosidase, an α-D-glucuronidase, an acetyl-xylan    esterase, a feruloyl esterase, a coumaroyl esterase, an    α-galactosidase, a β-galactosidase, a β-mannanase or a    β-mannosidase.-   12. A composition according to any one of the embodiments 9 to 11,    wherein the composition is a whole fermentation broth.-   13. Process for degrading cellulosic material, the process    comprising the step of contacting the cellulosic material with a    polypeptide according to embodiment 1 or a composition according to    any one of the embodiments 9 to 12.-   14. Process for producing a fermentation product, the process    comprising the steps of:    -   (d) enzymatically hydrolysing a cellulosic material with a        polypeptide according to embodiment 1 or a composition according        to any one of the embodiments 9 to 12,    -   (e) fermenting the enzymatically hydrolysed cellulosic material        to produce a fermentation product, and    -   (f) optionally, recovering of the fermentation product.-   15. Process according to embodiment 14, wherein the fermentation    product is an alcohol, such as ethanol.

A reference herein to a patent document or other matter which is givenas prior art is not to be taken as an admission that that document ormatter was known or that the information it contains was part of thecommon general knowledge as at the priority date of any of the claims.

The disclosure of each reference set forth herein is incorporated hereinby reference in its entirety.

The present invention is further illustrated by the following Examples:

EXAMPLES General Procedures and Molecular Biology Techniques

Standard molecular cloning techniques such as DNA isolation, gelelectrophoresis, enzymatic restriction modifications of nucleic acids,E. coli transformation e.a., were performed as described by Sambrook etal., 1989 (2nd ed) and 2001 (3rd ed), Molecular cloning: a laboratorymanual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.and Innes et al. (1990) PCR protocols, a guide to methods andapplications, Academic Press, San Diego. Examples of the general designof expression vectors for gene overexpression and disruption vectors fordown-regulation, transformation, use of markers, strains and selectivemedia can be found in WO 1998/46772, WO 1999/32617, WO 2001/121779, WO2005/095624, WO 2006/040312, EP 0 635 574B, WO 2005/100573, WO2011/009700, WO 2012/001169, WO 2013/135729, WO 2014/013073, WO2014/013074 and WO 2005/100573. After transformation, the removal of theselection marker by a (second) homologous recombination event isperformed by using a recombinase such as detailed in WO2013135729.

Preparation of Pre-Treated, Corn Stover Substrate.

Dilute-acid pre-treated corn stover was obtained as described in Schell,D. J., Applied Biochemistry and Biotechnology (2003), vol. 105-108, pp69-85. A pilot scale pretreatment reactor was used operating at steadystate conditions of 190° C., 1 min residence time and an effective H2SO4acid concentration of 1.45% (w/w) in the liquid phase. For thepreparation of low acid pretreated corn stover, also referred to asmildly pretreated corn stover, a pilot scale pretreatment reactor wasused operating at steady state conditions of 182° C., 4.7 min residencetime and an effective H2SO4 acid concentration of 0.35% (w/w) in theliquid aiming at a pH of 2.5.

Example 1: Cloning of LPMO Variants in A. niger and Generation of EnzymeSamples Strains

WT 1: This A. niger strain is used as a wild-type strain. This strain isdeposited at the CBS Institute under the deposit number CBS 513.88.

WT 2: This A. niger strain is a WT 1 strain comprising a deletion of thegene encoding glucoamylase (glaA). WT 2 was constructed by using the“MARKER-GENE FREE” approach as described in EP 0 635 574 B1. In thispatent, it is extensively described how to delete glaA specific DNAsequences in the genome of CBS 513.88. The procedure resulted in aMARKER-GENE FREE ΔglaA recombinant A. niger CBS 513.88 strain,possessing finally no foreign DNA sequences at all.

WT 3: This A. niger strain is a WT 2 strain comprising a deletion of thepepA gene encoding the major extracellular aspartic protease PepA. TheWT 3 strain is constructed by using the “MARKER-GENE FREE” approach asdescribed in EP 0 635 574. The method described in this patent is usedto delete pepA specific DNA sequences in the genome of WT 2, asdescribed by van den Hombergh et al. (van den Hombergh J P, SollewijnGelpke M D, van de Vondervoort P J, Buxton F P, Visser J.(1997)—Disruption of three acid proteases in Aspergillus niger—effectson protease spectrum, intracellular proteolysis, and degradation oftarget proteins—Eur J Biochem. 247(2): 605-13). The procedure resultedin a MARKER-GENE FREE WT 3 strain, with the pepA gene inactivated in theWT 2 strain background.

WT 4: This A. niger strain is a WT 3 strain comprising the deletion ofthree genes encoding alpha-amylases (amyB, amyBI and amyBII) in threesubsequent steps. The construction of deletion vectors and genomicdeletion of these three genes has been described in detail in WO2005/095624. The vectors pDEL-AMYA, pDEL-AMYBI and pDEL-AMYBII,described in WO 2005/095624, have been used according the “MARKER-GENEFREE” approach as described in EP 0 635 574 B1. The procedure describedabove resulted in an oxalate deficient, MARKER-GENE FREE ΔglaA, pepA,ΔamyA, ΔamyBI and ΔamyBII glucoamylase-, acid protease-,amylase-negative recombinant A. niger CBS 513.88 (WT 1) strain,possessing finally no foreign DNA sequences at all. As such, WT 4 has alow (gluco-)amylase background and is more optimized for enzymeexpression and expression detection compared to WT 1.

Cloning and Expression of the Polypeptides of the Invention

The protein sequence of the polypeptides of the invention is shown inSEQ ID NO: 1, 4, 7, 10, 13, 16, 19 and 22 and SEQ ID NO: 2, 5, 8, 11,14, 17, 20 and 23 (mature part).

For the polypeptides of the invention, codon-adapted DNA sequence forexpression of the protein in Aspergillus niger was designed containingadditional BsaI type II restriction enzyme sites to enable subcloning inthe Aspergillus expression vector pGBFIN-50 (see FIG. 1). Codonadaptation was performed as described in WO 2008/000632. The codonoptimized DNA sequences for expression of the genes encoding thepolypeptides of the invention in A. niger is shown in SEQ ID NO: 3, 6,9, 12, 15, 18, 21 and 24.

The translational initiation sequence of the glucoamylase glaA promoterwas modified into 5′-CACCGTCAAAATG-3′, already present in theAspergillus expression vector pGBFIN-50, and an optimal translationaltermination sequence 5′-TAAA-3′ was used in the generation of theexpression constructs (as also detailed in WO 2006/077258 and WO2011/009700). The DNA sequence coding for the LMPO variant enzyme of theinvention was synthesized completely (DNA2.0, Menlo Park, USA) andcloned into Aspergillus niger expression vector pGBFIN-50 throughrepetitive steps of BsaI digestion and ligation (US 2015/0050696)according to standard procedures.

Subsequently, A. niger WT4 was transformed with a PCR-amplifiedPgla-3′gla fragment generated using the above described vectorsresulting from the GoldenGate cloning as template. The PCR fragments arecomprising the LMPO expression cassette under control of theglucoamylase promoter and the hygromycin selection marker.Alternatively, a NotI-digested and purified fragment of the GoldenGatederived LMPO variant expression vector, containing the LMPO variantexpression cassette individually and the hygromycin selection markercould have been used. Transformation experiments were performed withstrain and methods as described in WO 1998/46772, WO 1999/32617, WO2011/009700, WO 2012/001169, WO 2013/135729, WO 2014/013073 and WO2014/013074 and references therein. After transformation, theprotoplasts were plated onto selective regeneration medium consisting ofAspergillus minimal medium supplemented with 60 μg/ml Hygromycin B.After incubation for 5-10 days at 30° C., single transformants wereisolated on PDA (Potato Dextrose Agar, supplemented with 60 μg/mlHygromycin B. After 5-7 days growth at 30° C. single transformants wereused for fermentations.

Aspergillus niger Shake Flask Fermentation

About 107 spores of selected transformants and control strains wereinoculated into 100 ml shake flasks with baffles containing 20 ml ofliquid pre-culture medium consisting of per liter: 30 g maltose.H2O; 5 gyeast extract; 10 g hydrolyzed casein; 1 g KH2PO4; 0.5 g MgSO4.7H2O;0.03 g ZnCl2; 0.02 g CaCl₂); 0.01 g MnSO4.4H2O; 0.3 g FeSO4.7H2O; 3 gTween-80; 10 ml penicillin (5000 IU/ml)/Streptomycin (5000 UG/ml);0.0025 g CuSO4; pH 5.5. These cultures were grown at 34 degrees Celsius(and 170 rpm) for 16-24 hours. 10 ml of this culture was inoculated into500 ml shake flasks with baffles containing 100 ml fermentation mediumconsisting of per liter: 70 g glucose.H2O; 25 g hydrolyzed casein; 12.5g yeast extract; 1 g KH2PO4; 2 g K2SO4; 0.5 g MgSO4.7H2O; 0.03 g ZnCl2;0.02 g CaCl₂); 0.009 g MnSO4.1H2O; 0.003 g FeSO4.7H2O; 10 ml penicillin(5000 IU/ml)/Streptomycin (5000 UG/ml); 0.0025 g CuSO4; adjusted topH5.6. These cultures were grown at 34 degrees Celsius (and 170 rpm)until all glucose was depleted (usually after 4-7 days). Samples takenfrom the fermentation broth were centrifuged (10 min at 5000×g) in aswinging bucket centrifuge and supernatants collected and filtered overa 0.2 μm filter (Nalgene)

Shake Flask Concentration and Protein Concentration Determination withTCA-Biuret Method

In order to obtain greater amounts of material for further testing, thefermentation supernatants obtained as described above (volume between 75and 100 ml) were concentrated using a 10 kDa spin filter to a volume ofapproximately 5 ml. Subsequently, the protein concentration in theconcentrated supernatant was determined via a TCA-biuret method.

Concentrated protein samples (supernatants) were diluted with water to aconcentration between 2 and 8 mg/ml. Bovine serum albumin (BSA)dilutions (0, 1, 2, 5, 8 and 10 mg/ml) were made and included as samplesto generate a calibration curve. Of each diluted protein sample 270 μlwas transferred into a 10 ml tube containing 830 μl of a 12% (w/v)trichloro acetic acid solution in acetone and mixed thoroughly.Subsequently, the tubes were incubated on ice water for one hour andcentrifuged for 30 minutes, at 4° C. and 6000 rpm. The supernatant wasdiscarded and pellets were dried by inverting the tubes on a tissue andletting them stand for 30 minutes at room temperature. Next, 3 mlBioQuant Biuret reagent mix was added to the pellet in the tube and thepellet was solubilized upon mixing followed by addition of 1 ml water.The tube was mixed thoroughly and incubated at room temperature for 30minutes. The absorption of the mixture was measured at 546 nm with awater sample used as a blank measurement and the protein concentrationwas calculated via the BSA calibration line.

Example 2: Cloning of a LPMO Variant in Rasamsonia LPMO Knockout Strainand Generation of Enzyme Sample Strains and Enzymes

The Rasamsonia emersonii (R. emersonii) strains used herein are derivedfrom ATCC16479, which is used as wild-type strain. ATCC16479 wasformerly also known as Talaromyces emersonii and Penicillium geosmithiaemersonii. Upon the use of the name Rasamsonia emersonii alsoTalaromyces emersonii is meant. Other strain designations of R.emersonii MCC 16479 are CBS393.64, IF031232 and IM11 16815. Rasamsonia(Talaromyces) emersonii strain TEC-142 is deposited at CENTRAAL BUREAUVOOR SCHIMMELCULTURES, Uppsalalaan 8, P.O. Box 85167, NL-3508 ADUtrecht, The Netherlands on 1 Jul. 2009 having the Accession Number CBS124902. TEC-142S is a single isolate of TEC-142.

Molecular Biology Techniques

In this strain, using molecular biology techniques known to the skilledperson (see: Sambrook & Russell, Molecular Cloning: A Laboratory Manual,3rd Ed., CSHL Press, Cold Spring Harbor, N.Y., 2001), a LPMO knock-outderivative strain was obtained and subsequently used to over express apolypeptide of the invention as described below. Examples of the generaldesign of expression vectors for gene over expression and disruptionvectors, transformation, use of markers and selective media can be foundin for example WO 1998/46772, WO 1999/32617, WO 2001/121779, WO2005/095624, EP 0 635 574B and WO 2005/100573.

Transformation of R. emersonii with pDEL_Phleo Knock-Out Construct

In order to obtain a LPMO deletion derivative, R. emersonii wastransformed with a PCR amplified fragment derived from pDel-Phleoconstruct. This PCR fragment consists of 2.8 kb upstream (including 800bp native LPMO promoter) and 2.0 kb downstream sequences of the nativeR. emersonii LPMO gene. In between these flanking sequences is alox-flanked phleomycin resistance gene located. After transformation anda homologous recombination event the native LPMO gene including thefirst 800 bp are exchanged by the lox-flanked phleomycin resistancegene.

R. emersonii transformation was performed according to the protocoldescribed in WO 2011/054899. Transformants were selected on platescontaining phleomycine and subsequently confirmed by qPCR.

Cloning and Expression of the Polypeptides of the Invention in Remersonii

The protein sequence of the polypeptides of the invention is set out inSEQ ID NO: 25, 28, 31, 34, 37, 40, 43 and 46 and SEQ ID NO: 26, 29, 32,35, 38, 41, 44 and 47 (mature part).

For the polypeptides of the invention, codon-adapted DNA sequence forexpression of the protein in R. emersonii was designed containingadditional BsaI type II restriction enzyme sites to enable subcloning,together with the native LPMO promoter and terminator sequences in astandard cloning vector (ef.bbn). The DNA sequences coding for thepolypeptides of the invention, as well as the 2.8 kb upstream (includingthe 800 bp native LPMO promoter sequences) and 2.0 kb downstreamsequences flanking the native LPMO gene were synthesized completely(DNA2.0, Menlo Park, USA) and cloned into the ef.bbn vector throughrepetitive steps of BsaI digestion and ligation (US 2015/0050696)according standard procedure resulting in a LPMO variant expressingconstruct.

Subsequently, the above described R. emersonii LPMO deletion strain wasco-transformed with above described PCR-amplified LPMO expressionfragments and a lox-flanked hygromycin resistance gene fragment.

Transformants are selected on plates containing hygromycin antibioticmarker and subsequent qPCR analyzed on the presence of a polypeptide ofthe invention. Transformants with the correct characteristics weresubsequently transformed with a pEBA521 vector (see FIG. 2) totransiently express the cre-recombinase enzyme to remove the lox-flankedhygromycin resistance gene by recombination over the lox66 and lox71site.

Construction of the Cre-Recombinase Expression Vector

pEBA521 was constructed by DNA2.0 (Menlo Park, USA) and contains thefollowing components: expression cassette consisting of the A. nigerglaA promoter, ORF encoding cre-recombinase (AAY56380) and A. nidulansniaD terminator; expression cassette consisting of the A. nidulans gpdApromoter, ORF encoding hygromycin B resistance protein and P.chrysogenum penDE terminator (Genbank: M31454.1, nucleotides 1750-2219);pAMPF21 derived vector containing the AMA1 region and the CATchloramphenicol resistance gene.

Shake Flask Media for Rasamsonia

Rasamsonia medium 1: per litre: Glucose 20 g; Yeast extract (Difco) 20g; Clerol FBA3107 (AF) 4 drops; MES 30 g; pH 6.0; Sterilize 20 min at120° C.

Rasamsonia medium 2: per litre: Salt fraction no. 3 10 g; glucose 10 g;KH2PO4 5 g; NaH2PO4 2 g; (NH4)2SO4 5 g; MES 30 g; pH 5.4; Sterilize 20min at 120° C.

Rasamsonia medium 3: per litre: Salt fraction no. 3 10 g; cellulose 20g; KH2PO4 5 g; NaH2PO4 2 g; (NH4)2SO4 5 g; MES 30 g; pH 5.4; Sterilize20 min at 120° C.

Rasamsonia medium 4: per litre: Salt fraction no. 3 10 g; cellulose 15g; glucose 5 g; KH2PO4 5 g; NaH2PO4 2 g; (NH4)2SO4 5 g; MES 30 g; pH5.4; Sterilize 20 min at 120° C.

Spore Batch Preparation for Rasamsonia

Strains were grown from stocks on Rasamsonia agar medium in 10 cmdiameter Petri dishes for 5-7 days at 40° C. For MTP fermentations,strains were grown in 96-well plates containing Rasamsonia agar medium.Strain stocks were stored at −80° C. in 10% glycerol.

Shake Flask Growth Protocol of Rasamsonia

Spores were inoculated into 100 ml shake flasks containing 20 ml ofRasamsonia medium 1 and incubated at 45° C. at 250 rpm in an incubatorshaker for 1 day (preculture 1) and 1 or 2 ml of biomass from preculture1 was transferred to 100 ml shake flasks containing 20 ml of Rasamsoniamedium 2 and grown under conditions as described above for 1 day(preculture 2). Subsequently, 1 or 2 ml of biomass from preculture 2 wastransferred to 100 ml shake flasks containing 20 ml of Rasamsonia medium3 or 4 and grown under conditions described above for 3 days.

Protein Concentration Determination with TCA-Biuret Method

Protein samples (Rasamsonia supernatants) were diluted with water to aconcentration between 2 and 8 mg/ml. Bovine serum albumin (BSA)dilutions (0, 1, 2, 5, 8 and 10 mg/ml) were made and included as samplesto generate a calibration curve. Of each diluted protein sample 270 μlwas transferred into a 10 ml tube containing 830 μl of a 12% (w/v)trichloro acetic acid solution in acetone and mixed thoroughly.Subsequently, the tubes were incubated on ice water for one hour andcentrifuged for 30 minutes, at 4° C. and 6000 rpm. The supernatant wasdiscarded and pellets were dried by inverting the tubes on a tissue andletting them stand for 30 minutes at room temperature. Next, 3 mlBioQuant Biuret reagent mix was added to the pellet in the tube and thepellet was solubilized upon mixing followed by addition of 1 ml water.The tube was mixed thoroughly and incubated at room temperature for 30minutes. The absorption of the mixture was measured at 546 nm with awater sample used as a blank measurement and the protein concentrationwas calculated via the BSA calibration line.

Example 3: Cellulolytic Enhancing Activity Assay

The cellulolytic enhancing activity of the polypeptides of the inventionproduced according to Example 1 was analyzed as follows; theconcentrated supernatant of an A. niger shake flask fermentationexpressing a polypeptide of the invention was spiked on top of a 3E baseenzyme mix. The 3E base enzyme mix was dosed at a concentration of 1.6mg/g dry matter weight in the hydrolysis reaction and was composed of:beta-glucosidase (BG) at 0.225 mg/g dry matter weight, cellobiohydrolaseI (CBHI) at 0.75 mg/g dry matter weight and cellobiohydrolase II (CBHII)at 0.625 mg/g dry matter weight (see WO 2011/098577 for details of theseenzymes and their production).

The polypeptide containing supernatant was spiked on top of this 3E basemix in a final concentration of 0.9 mg of the polypeptide/g dry matterweight. The hydrolysis performance of these four enzyme mixes werecompared by analyzing mono sugar release from a low acid pretreated cornstover feedstock in a concentration of 7.5% dry matter weight after anincubation of 72 hours at 62° C., pH 4.5 (pH of feedstock was adjustedto 4.5 with a 4 M NaOH solution). The hydrolysis reactions wereperformed in a total volume of 20 g in 40 ml centrifuge bottles (NalgeneOakridge) which were incubated in an oven incubator (Techne HB-1Dhybridization oven), while rotating at set-point 3. As blank control,the 3 enzyme base mix (BG, CBHI and CBHII) with addition of waterinstead of a polypeptide of the invention was incubated with feedstockunder the same conditions as described above and mono sugar release wasmeasured. All experiments were performed in duplicate. After incubation,the samples were centrifuged and soluble sugars were analyzed by HPLC asfollows.

The sugar content of the samples after enzymatic hydrolysis wereanalyzed using a High-Performance Liquid Chromatography System (Agilent1100) equipped with a refection index detector (Agilent 1260 Infinity).The separation of the sugars was achieved by using a 300×7.8 mm AminexHPX-87P (Bio rad cat no 125-0098) column; Pre-column: Micro guardCarbo-P (Bio Rad cat no 125-0119); mobile phase was HPLC grade water;flow rate of 0.6 ml/min and a column temperature of 85° C. The injectionvolume was 10 μl. The samples were diluted with HPLC grade water to amaximum of 2.5 g/l glucose and filtered by using 0.2 μm filter (AfridiscLC25 mm syringe filter PVDF membrane). The glucose was identified andquantified according to the retention time, which was compared to theexternal glucose standard (D-(+)-Glucose, Sigma cat no: G7528) rangingfrom 0.2; 0.4; 1.0; 2.0 g/l.

The data presented in Table 1 show that addition of the polypeptide ofthe invention to the 3E base mix significantly improves the glucoserelease from the low acid pretreated corn stover feedstock.

TABLE 1 Glucose released by 3E base mix and 3E base mix spiked withpolypeptide of the invention from low acid pretreated corn stover aftera 72 hrs incubation at 62° C. at pH 4.5 Enzyme mix Glucose (g/l) 3E basemix 5.29 3E base mix + polypeptide of invention (SEQ ID NO: 1 and SEQ IDNO: 2) 7.1 3E base mix + polypeptide of invention (SEQ ID NO: 4 and SEQID NO: 5) 7.3 3E base mix + polypeptide of invention (SEQ ID NO: 7 andSEQ ID NO: 8) 6.7 3E base mix + polypeptide of invention (SEQ ID NO: 10and SEQ ID NO: 11) 6.9 3E base mix + polypeptide of invention (SEQ IDNO: 13 and SEQ ID NO: 14) 7.7 3E base mix + polypeptide of invention(SEQ ID NO: 16 and SEQ ID NO: 17) 8 3E base mix + polypeptide ofinvention (SEQ ID NO: 19 and SEQ ID NO: 20) 7.4 3E base mix +polypeptide of invention (SEQ ID NO: 22 and SEQ ID NO: 23) 7

Example 4: Activity Assay Using Artificial Substrate AZO-Xyloglucan

The activity of the polypeptides of the invention produced according toExample 1 was also tested in an assay using AZO-xyloglucan (obtainedfrom Megazyme) as a substrate. A 1% Azo-xyloglucan substrate wasprepared by adding 1 g of AZO-xyloglucan to 80 ml of miliQ-water. Thesolution was subsequently vigorously stirred for about 20 minutes and 5ml of a 2M sodium acetate solution was added. Subsequently the pH wasadjusted to 4.5 using 3 ml 4M NaOH and the volume was set to 100 ml withmilliQ-water. After pre-heating 400 μl of this 1% AZO-xyloglucansolution to 37° C., the polypeptides of the invention and a wild-typereference (concentrations ranging from 0.05-2 mg/ml) and 10 mM vitamin C(or other electron donors like cysteine and dithiothreitol) were addedto a final volume of 200 μl. The mixture (0.6 ml) was incubated for 4hours in an Eppendorf®-thermomixer at 37° C. After the incubation, thereaction was terminated by the addition of 1 ml 96% ethanol. Thesuspension was mixed vigorously for 10 seconds on a vortex mixer andsubsequently centrifuged for 10 minutes at 1000×g at 20° C. Thesupernatant was pipetted into a cuvette and the absorbance at awavelength of 590 nm was determined with a spectrophotometer, aftertaking a zero measurement with water.

For each experiment, a control was included where the enzyme sample wasreplaced by water but still containing the electron donor (vitamin C orcysteine or dithiothreitol) and the incubation of the AZO-xyloglucan wasperformed under the same conditions as described above. The absorptionof this control sample was subtracted from the absorption value of theenzyme incubations. The height of the absorbance of the samplecontaining the polypeptide of the invention minus the absorbance of thecontrol is a measurement for the activity of the enzyme; the higher theabsorbance, the higher the activity of the polypeptide of the inventionon this AZO-xyloglucan substrate.

The data in Table 2 show that the polypeptides of the invention are moreactive than a wild-type reference on this AZO-xyloglucan substrate when10 mM dithiothreitol, 10 mM vitamin C or 10 mM cysteine were used as anelectron donor and both enzymes were dosed at 0.08 mg/ml.

TABLE 2 Absorbance at 590 as indicator for LPMO activity; wild-typeenzyme and polypeptides of the invention in AZO-xyloglucan assay with 10mM dithiothreitol, 10 mM vitamin C or 10 mM cysteine as electron donor590 nm (AU) 10 mM 10 mM 10 mM Enzyme dithiothreitol vitamin C cysteineWild-type reference 1 0.25 0.75 0.44 Polypeptide of invention — 0.85 —(SEQ ID NO: 1 and SEQ ID NO: 2) Polypeptide of invention 0.26 — — (SEQID NO: 4 and SEQ ID NO: 5) Polypeptide of invention 0.32 0.94 — (SEQ IDNO: 7 and SEQ ID NO: 8) Polypeptide of invention 0.34 — 0.47 (SEQ ID NO:10 and SEQ ID NO: 11) Wild-type reference 2 0.17 — 0.36 Polypeptide ofinvention 0.26 — — (SEQ ID NO: 13 and SEQ ID NO: 14) Polypeptide ofinvention — — — (SEQ ID NO: 16 and SEQ ID NO: 17) Polypeptide ofinvention 0.31 — 0.47 (SEQ ID NO: 19 and SEQ ID NO: 20) Polypeptide ofinvention 0.40 — 0.48 (SEQ ID NO: 22 and SEQ ID NO: 23)

This AZO-xyloglucan activity assay described in this Example may be usedto test the activity of the polypeptides of the invention underdifferent conditions. The following parameters, for example, can bevaried: replacement of vitamin C, dithiothreitol or cysteine for anotherelectron donor in a different concentration, the incubation temperature,the pH, the presence of an inhibitor like for example gluconic acid orglucose, or with and without a preincubation at a certain temperature orin the presence of a certain compound like for example peroxide.

Example 5: Sugar-Release Activity Assay from (Mildly) Acid PretreatedCorn Stover Feedstock

The cellulolytic activity of the polypeptides of the invention producedaccording to Example 2 is analyzed as follows; the supernatant of theshake flask fermentation of the Rasamsonia strain expressing thepolypeptides of the invention is incubated in the presence of a low acidpretreated feedstock and the glucose release is monitored compared to areference strain lacking the polypeptides of the invention.

In this experiment, the typical low acid pretreated corn stoverconcentration is between 5% and 10% dry matter. The Rasamsonia shakeflask supernatant containing the polypeptide of the invention and thecontrol supernatant without the polypeptide of the invention areincubated with the feedstock at a total protein dosage of 2.5 mg/g drymatter during the hydrolysis reaction. The hydrolysis reactions aretypically performed in a total volume of 20 g in 40 ml centrifugebottles (Nalgene Oakridge) and are incubated in an oven incubator(Techne HB-1 D hybridization oven) while rotating at set-point 3. Afterincubation for 72 hours at pH 4.5 at 62° C., the hydrolysis performanceof the Rasamsonia supernatants are compared by analyzing mono sugarrelease from the low acid pretreated corn stover feedstock. After theincubation, the samples are centrifuged and soluble sugars are analyzedby HPLC as follows.

The sugar content of the samples after enzymatic hydrolysis is analyzedusing a High-Performance Liquid Chromatography System (Agilent 1100)equipped with a refection index detector (Agilent 1260 Infinity). Theseparation of the sugars is achieved by using a 300×7.8 mm AminexHPX-87P (Bio rad cat no 125-0098) column; Pre-column: Micro guardCarbo-P (Bio Rad cat no 125-0119); mobile phase is HPLC grade water;flow rate of 0.6 ml/min and a column temperature of 85° C. The injectionvolume is 10 The samples are diluted with HPLC grade water to a maximumof 2.5 g/l glucose and filtered by using 0.2 μm filter (Afridisc LC25 mmsyringe filter PVDF membrane). The glucose is identified and quantifiedaccording to the retention time, which is compared to the externalglucose standard (D-(+)-Glucose, Sigma cat no: G7528) ranging from 0.2;0.4; 1.0; 2.0 g/l.

The data show that the polypeptides of the invention have a higherglucose release from the low acid pretreated corn stover feedstock.

1. A polypeptide having cellulolytic enhancing activity, wherein thepolypeptide is selected from the group consisting of: (a) a polypeptidecomprising an amino acid sequence having at least 90% sequence identitywith the amino acid sequence of SEQ ID NO:5; (b) a polypeptide encodedby a polynucleotide comprising a nucleotide sequence having at least 90%sequence identity to the nucleotide sequence of SEQ ID NO:6; (c) apolypeptide encoded by a polynucleotide comprising a nucleotide sequencewhich hybridises under at least high stringency conditions with thecomplementary strand of SEQ ID NO:6; and (d) a fragment of thepolypeptide of (a), (b), or (c), that has cellulolytic enhancingactivity.
 2. A polynucleotide, wherein the polynucleotide comprises anucleotide sequence that is selected from the group consisting of: (a) anucleotide sequence having at least 90% sequence identity with thenucleotide sequence of SEQ ID NO:6, (b) a nucleotide sequence whichhybridises under at least high stringency conditions with thecomplementary strand of SEQ ID NO:6, (c) a fragment which is at least100 nucleotides in length of a nucleotide sequence as defined in (a) or(b), (d) a nucleotide sequence which is degenerate as a result of thegenetic code to a nucleotide sequence as defined in any one of (a), (b),or (c), and (e) a nucleotide sequence which is the complement of anucleotide sequence as defined in (a), (b), (c), or (d).
 3. Thepolynucleotide according to claim 2, which encodes a polypeptideselected from the group consisting of: (a) a polypeptide comprising anamino acid sequence having at least 90% sequence identity with the aminoacid sequence of SEQ ID NO:5; (b) a polypeptide encoded by apolynucleotide comprising a nucleotide sequence having at least 90%sequence identity to the nucleotide sequence of SEQ ID NO:6; (c) apolypeptide encoded by a polynucleotide comprising a nucleotide sequencewhich hybridises under at least high stringency conditions with thecomplementary strand of SEQ ID NO:6; and (d) a fragment of thepolypeptide of (a), (b), or (c), that has cellulolytic enhancingactivity.
 4. A nucleic acid construct comprising the polynucleotideaccording to claim
 2. 5. The nucleic acid construct according to claim 4which is an expression vector, wherein the polynucleotide is operablylinked to at least one control sequence for the expression of thepolynucleotide in a host cell.
 6. A host cell comprising the polypeptideaccording to claim
 1. 7. The host cell according to claim 6 which is afungal cell.
 8. A process for producing the polypeptide according toclaim 1, which process comprises: (a) cultivating a host cell comprisingthe polypeptide under conditions conducive to the production of thepolypeptide, and (b) optionally, recovering the polypeptide.
 9. Acomposition comprising: (a) the polypeptide according to claim 1, and(b) a cellulase and/or a hemicellulase and/or a pectinase.
 10. Thecomposition according to claim 9, wherein the cellulase is acellobiohydrolase I, a cellobiohydrolase II, an endo-β-1,4-glucanase, aβ-glucosidase or a β-(1,3)(1,4)-glucanase.
 11. The composition accordingto claim 9, wherein the hemicellulase is an endoxylanase, aβ-xylosidase, an α-L-arabinofuranosidase, an α-D-glucuronidase, anacetyl-xylan esterase, a feruloyl esterase, a coumaroyl esterase, anα-galactosidase, a β-galactosidase, a β-mannanase or a β-mannosidase.12. The composition according to claim 9, wherein the composition is awhole fermentation broth.
 13. A process for degrading cellulosicmaterial, the process comprising contacting the cellulosic material withthe polypeptide according to claim
 1. 14. A process for producing afermentation product, the process comprising: (a) enzymaticallyhydrolysing a cellulosic material with the polypeptide according toclaim 1; (b) fermenting the enzymatically hydrolysed cellulosic materialto produce the fermentation product; and (c) optionally, recovering thefermentation product.
 15. The process according to claim 14, wherein thefermentation product is an alcohol, optionally ethanol.
 16. A host cellcomprising the polynucleotide according to claim
 2. 17. A process fordegrading cellulosic material, the process comprising contacting thecellulosic material with the composition according to claim
 9. 18. Aprocess for producing a fermentation product, the process comprising:(a) enzymatically hydrolysing a cellulosic material with the compositionaccording to claim 9; (b) fermenting the enzymatically hydrolysedcellulosic material to produce the fermentation product; and (c)optionally, recovering the fermentation product.